6-139486909-C-T

Variant names:

• chr6-139486909-C-T
• rs1468708
• ENST00000647815.1:n.134+294C>T

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+294C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.671 in 152,074 control chromosomes in the GnomAD database, including 35,005 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 0.67 (35005 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 4 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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
ENSG00000226571	ENST00000647815.1	n.134+294C>T		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000647987.2	n.212+294C>T		intron_variant	Intron 1 of 1
ENSG00000226571	ENST00000650173.1	n.1279-19555C>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.671 AC: 101915 AN: 151956 Hom.: 34967 Cov.: 32

Gnomad AFR AF: 0.814

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.705

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.671 AC: 102008 AN: 152074 Hom.: 35005 Cov.: 32 AF XY: 0.670 AC XY: 49814 AN XY: 74310

African (AFR) AF: 0.814 AC: 33763 AN: 41496

American (AMR) AF: 0.603 AC: 9195 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.605 AC: 2095 AN: 3464

East Asian (EAS) AF: 0.783 AC: 4062 AN: 5186

South Asian (SAS) AF: 0.457 AC: 2195 AN: 4804

European-Finnish (FIN) AF: 0.705 AC: 7452 AN: 10576

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.605 AC: 41157 AN: 67982

Other (OTH) AF: 0.640 AC: 1349 AN: 2108

Alfa AF: 0.610 Hom.: 15274

Bravo AF: 0.675

Asia WGS AF: 0.593 AC: 2061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.50
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1468708; hg19: chr6-139808046; COSMIC: COSV60286761;