6-139512875-T-G

Variant names:

• chr6-139512875-T-G
• rs632057
• ENST00000647815.1:n.134+26260T>G

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+26260T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,976 control chromosomes in the GnomAD database, including 24,825 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 0.57 (24825 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694
• Publications: 30 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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.696 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+26260T>G		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000775574.1	n.194-34367T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85854 AN: 151858 Hom.: 24797 Cov.: 32

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.565 AC: 85933 AN: 151976 Hom.: 24825 Cov.: 32 AF XY: 0.565 AC XY: 41990 AN XY: 74254

African (AFR) AF: 0.470 AC: 19465 AN: 41438

American (AMR) AF: 0.588 AC: 8974 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3472

East Asian (EAS) AF: 0.307 AC: 1591 AN: 5184

South Asian (SAS) AF: 0.716 AC: 3447 AN: 4816

European-Finnish (FIN) AF: 0.545 AC: 5751 AN: 10548

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42389 AN: 67952

Other (OTH) AF: 0.583 AC: 1231 AN: 2110

Alfa AF: 0.605 Hom.: 123222

Bravo AF: 0.559

Asia WGS AF: 0.538 AC: 1869 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.43
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs632057; hg19: chr6-139834012;