chr6-126942389-T-C

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650648.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650648.1		n.699+997A>G		intron	N/A
	ENSG00000293110	ENST00000650684.1		n.864-22743A>G		intron	N/A
	ENSG00000293110	ENST00000650727.1		n.730-22743A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1343657;

hg19: chr6-127263534;

COSMIC: COSV69425753;