6-139518286-C-A

Variant names:

• chr6-139518286-C-A
• rs643381
• ENST00000647815.1:n.134+31671C>A

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+31671C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 151,370 control chromosomes in the GnomAD database, including 14,765 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 0.41 (14765 hom., cov: 31)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.279
• Publications: 34 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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 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+31671C>A		intron_variant	Intron 1 of 2
ENSG00000226571	ENST00000775574.1	n.194-28956C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62256 AN: 151252 Hom.: 14751 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.411 AC: 62280 AN: 151370 Hom.: 14765 Cov.: 31 AF XY: 0.413 AC XY: 30542 AN XY: 73918

African (AFR) AF: 0.167 AC: 6886 AN: 41140

American (AMR) AF: 0.483 AC: 7347 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1864 AN: 3472

East Asian (EAS) AF: 0.271 AC: 1389 AN: 5118

South Asian (SAS) AF: 0.652 AC: 3137 AN: 4808

European-Finnish (FIN) AF: 0.453 AC: 4732 AN: 10436

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35370 AN: 67872

Other (OTH) AF: 0.432 AC: 904 AN: 2092

Alfa AF: 0.480 Hom.: 67614

Bravo AF: 0.395

Asia WGS AF: 0.469 AC: 1630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.89
DANN	Benign	0.77
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs643381; hg19: chr6-139839423; COSMIC: COSV69428629;