dbSNP rs936503: ENSG00000265101:n.128C>T (chr18-78927314-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000580639.1(ENSG00000265101):n.128C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,228 control chromosomes in the GnomAD database, including 22,034 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 22026 hom., cov: 35)

Exomes 𝑓: 0.79 ( 8 hom. )

Consequence

ENSG00000265101
ENST00000580639.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.128

Publications

4 publications found

Variant links:

Genes affected

ENSG00000265101 (HGNC:):

ENSG00000265101 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.03).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372224	XR_935678.3 link	n.60C>T		non_coding_transcript_exon_variant	Exon 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000265101	ENST00000580639.1 link	n.128C>T		non_coding_transcript_exon_variant	Exon 1 of 2	3
ENSG00000287758	ENST00000654461.1 link	n.437+11G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80485

AN:

152082

Hom.:

22024

Cov.:

show subpopulations

Gnomad AFR

AF:

0.394

Gnomad AMI

AF:

0.558

Gnomad AMR

AF:

0.494

Gnomad ASJ

AF:

0.602

Gnomad EAS

AF:

0.452

Gnomad SAS

AF:

0.436

Gnomad FIN

AF:

0.605

Gnomad MID

AF:

0.522

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.550

GnomAD4 exome

AF:

0.786

AC:

AN:

Hom.:

Cov.:

AF XY:

0.875

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.800

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.567

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:

0.529

AC:

80515

AN:

152200

Hom.:

22026

Cov.:

AF XY:

0.525

AC XY:

39100

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.394

AC:

16362

AN:

41524

American (AMR)

AF:

0.494

AC:

7549

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.602

AC:

2090

AN:

3470

East Asian (EAS)

AF:

0.451

AC:

2332

AN:

5170

South Asian (SAS)

AF:

0.436

AC:

2107

AN:

4830

European-Finnish (FIN)

AF:

0.605

AC:

6406

AN:

10596

Middle Eastern (MID)

AF:

0.517

AC:

152

AN:

294

European-Non Finnish (NFE)

AF:

0.615

AC:

41840

AN:

67996

Other (OTH)

AF:

0.553

AC:

1168

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1955

3910

5864

7819

9774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.589

Hom.:

114069

Bravo

AF:

0.519

Asia WGS

AF:

0.442

AC:

1534

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.6

(source)

DANN

Benign

0.45

PhyloP100

-0.13

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over