Genetic Variant ENSG00000301866:n.696C>T (chr7-150342466-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000563946.1(ENSG00000301866):n.696C>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 0.219 in 133,858 control chromosomes in the GnomAD database, including 3,611 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 0.22 ( 3609 hom., cov: 31)

Exomes 𝑓: 0.36 ( 2 hom. )

Consequence

ENSG00000301866
ENST00000563946.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.280

Publications

25 publications found

Variant links:

Genes affected

ENSG00000301866 (HGNC:):

ENSG00000301866 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986858	XR_001745420.3 link	n.493+129C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000301866	ENST00000563946.1 link	n.696C>T	non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000301866	ENST00000647589.1 link	n.413C>T	non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000301866	ENST00000782374.1 link	n.575C>T	non_coding_transcript_exon_variant	Exon 1 of 3

Frequencies

GnomAD3 genomes

AF:

0.219

AC:

29285

AN:

133788

Hom.:

3616

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0775

Gnomad AMI

AF:

0.398

Gnomad AMR

AF:

0.151

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.287

Gnomad SAS

AF:

0.287

Gnomad FIN

AF:

0.254

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.262

Gnomad OTH

AF:

0.212

GnomAD4 exome

AF:

0.364

AC:

AN:

Hom.:

Cov.:

AF XY:

0.357

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.333

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.219

AC:

29266

AN:

133836

Hom.:

3609

Cov.:

AF XY:

0.220

AC XY:

14467

AN XY:

65790

show subpopulations

African (AFR)

AF:

0.0775

AC:

1913

AN:

24692

American (AMR)

AF:

0.151

AC:

2201

AN:

14586

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

1084

AN:

3430

East Asian (EAS)

AF:

0.286

AC:

1476

AN:

5152

South Asian (SAS)

AF:

0.287

AC:

1379

AN:

4804

European-Finnish (FIN)

AF:

0.254

AC:

2667

AN:

10508

Middle Eastern (MID)

AF:

0.246

AC:

AN:

272

European-Non Finnish (NFE)

AF:

0.262

AC:

17721

AN:

67586

Other (OTH)

AF:

0.209

AC:

397

AN:

1898

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1133

2267

3400

4534

5667

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

324

648

972

1296

1620

<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:

0.223

Hom.:

3569

Bravo

AF:

0.176

Asia WGS

AF:

0.259

AC:

897

AN:

3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.93

(source)

DANN

Benign

0.49

PhyloP100

-0.28

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