rs643381

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-139518286-C-A
• chr6-139518286-C-G
• chr6-139518286-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.453

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.432

Alfa AF: 0.495 Hom.: 26140

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

Splicing

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

Publications

LitVar

Other links and lift over

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