6-137797778-T-C

Variant names:

• chr6-137797778-T-C
• rs631609
• ENST00000760385.1:n.108+1086A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000760385.1(ENSG00000299085):​n.108+1086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,182 control chromosomes in the GnomAD database, including 57,243 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 0.87 (57243 hom., cov: 32)
• Consequence: ENSG00000299085 ENST00000760385.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 7 publications found

Genes affected

ENSG00000299085 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299085	ENST00000760385.1	n.108+1086A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131838 AN: 152064 Hom.: 57221 Cov.: 32

Gnomad AFR AF: 0.871

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.849

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.863

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.867 AC: 131911 AN: 152182 Hom.: 57243 Cov.: 32 AF XY: 0.866 AC XY: 64407 AN XY: 74414

African (AFR) AF: 0.870 AC: 36133 AN: 41510

American (AMR) AF: 0.849 AC: 12971 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3470

East Asian (EAS) AF: 0.849 AC: 4395 AN: 5178

South Asian (SAS) AF: 0.882 AC: 4248 AN: 4816

European-Finnish (FIN) AF: 0.873 AC: 9251 AN: 10592

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59193 AN: 68010

Other (OTH) AF: 0.858 AC: 1815 AN: 2116

Alfa AF: 0.868 Hom.: 16394

Bravo AF: 0.864

Asia WGS AF: 0.833 AC: 2900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.49
DANN	Benign	0.45
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs631609; hg19: chr6-138118915;