rs1343657

Variant names:

• chr6-126942389-T-C
• rs1343657
• ENST00000650648.1:n.699+997A>G

Variant summary

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

The ENST00000650648.1(ENSG00000293110):​n.699+997A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,914 control chromosomes in the GnomAD database, including 12,276 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 0.39 (12276 hom., cov: 31)
• Consequence: ENSG00000293110 ENST00000650648.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344
• Publications: 4 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377989	XR_002956387.2	n.3716-22743A>G		intron_variant	Intron 7 of 13
LOC105377989	XR_007059743.1	n.880-22743A>G		intron_variant	Intron 6 of 8
LOC105377989	XR_007059744.1	n.880-22743A>G		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000650648.1	n.699+997A>G		intron_variant	Intron 5 of 7
ENSG00000293110	ENST00000650684.1	n.864-22743A>G		intron_variant	Intron 6 of 8
ENSG00000293110	ENST00000650727.1	n.730-22743A>G		intron_variant	Intron 5 of 14

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58535 AN: 151796 Hom.: 12273 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.385 AC: 58556 AN: 151914 Hom.: 12276 Cov.: 31 AF XY: 0.391 AC XY: 29015 AN XY: 74222

African (AFR) AF: 0.214 AC: 8860 AN: 41456

American (AMR) AF: 0.392 AC: 5976 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1715 AN: 3468

East Asian (EAS) AF: 0.665 AC: 3432 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2140 AN: 4810

European-Finnish (FIN) AF: 0.453 AC: 4761 AN: 10510

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30225 AN: 67932

Other (OTH) AF: 0.391 AC: 824 AN: 2106

Alfa AF: 0.394 Hom.: 2097

Bravo AF: 0.376

Asia WGS AF: 0.467 AC: 1624 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.0
DANN	Benign	0.66
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1343657; hg19: chr6-127263534; COSMIC: COSV69425753;