Genetic Variant SEMA3D:c.861+44_861+71delATATATATATATATATATATATATATAT (chr7-85055645-CATATATATATATATATATATATATATAT-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The NM_001384900.1(SEMA3D):c.861+44_861+71delATATATATATATATATATATATATATAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000225 in 159,808 control chromosomes in the GnomAD database, including 7 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000063 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00060 ( 7 hom. )

Consequence

SEMA3D
NM_001384900.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.718

Publications

1 publications found

Variant links:

Genes affected

SEMA3D (HGNC:10726): (semaphorin 3D) This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]

SEMA3D links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 7 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001384900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SEMA3D	NM_001384900.1	MANE Select	c.861+44_861+71delATATATATATATATATATATATATATAT	intron	N/A	NP_001371829.1
SEMA3D	NM_001384901.1		c.861+44_861+71delATATATATATATATATATATATATATAT	intron	N/A	NP_001371830.1
SEMA3D	NM_001384902.1		c.861+44_861+71delATATATATATATATATATATATATATAT	intron	N/A	NP_001371831.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
SEMA3D	ENST00000284136.11	TSL:5 MANE Select	c.861+44_861+71delATATATATATATATATATATATATATAT	intron	N/A	ENSP00000284136.6
SEMA3D	ENST00000444867.1	TSL:1	c.861+44_861+71delATATATATATATATATATATATATATAT	intron	N/A	ENSP00000401366.1
SEMA3D	ENST00000463315.1	TSL:2	n.49+44_49+71delATATATATATATATATATATATATATAT	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0000627

AC:

AN:

111640

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000330

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000104

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000666

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000535

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000602

AC:

AN:

48168

Hom.:

AF XY:

0.000755

AC XY:

AN XY:

27808

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

690

American (AMR)

AF:

0.00129

AC:

AN:

774

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

712

East Asian (EAS)

AF:

0.00

AC:

AN:

1038

South Asian (SAS)

AF:

0.00195

AC:

AN:

1024

European-Finnish (FIN)

AF:

0.00

AC:

AN:

1262

Middle Eastern (MID)

AF:

0.00

AC:

AN:

118

European-Non Finnish (NFE)

AF:

0.000516

AC:

AN:

40690

Other (OTH)

AF:

0.00269

AC:

AN:

1860

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.748

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000627

AC:

AN:

111640

Hom.:

Cov.:

AF XY:

0.0000386

AC XY:

AN XY:

51814

show subpopulations

African (AFR)

AF:

0.0000330

AC:

AN:

30340

American (AMR)

AF:

0.000104

AC:

AN:

9572

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2948

East Asian (EAS)

AF:

0.00

AC:

AN:

3618

South Asian (SAS)

AF:

0.000666

AC:

AN:

3004

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3644

Middle Eastern (MID)

AF:

0.00

AC:

AN:

208

European-Non Finnish (NFE)

AF:

0.0000535

AC:

AN:

56072

Other (OTH)

AF:

0.00

AC:

AN:

1456

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.711

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over