6-126642880-G-T

Variant names:

• chr6-126642880-G-T
• rs1538956
• ENST00000650727.1:n.1167-21007C>A

Variant summary

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

The ENST00000650727.1(ENSG00000293110):​n.1167-21007C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,984 control chromosomes in the GnomAD database, including 18,000 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 0.45 (18000 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000650727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 18 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650727.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000650727.1		n.1167-21007C>A		intron	N/A
	ENSG00000293110	ENST00000651326.1		n.694-39415C>A		intron	N/A
	ENSG00000293110	ENST00000652545.1		n.1477-21007C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68555 AN: 151866 Hom.: 17996 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.451 AC: 68560 AN: 151984 Hom.: 18000 Cov.: 32 AF XY: 0.462 AC XY: 34311 AN XY: 74296

African (AFR) AF: 0.208 AC: 8619 AN: 41466

American (AMR) AF: 0.624 AC: 9535 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3466

East Asian (EAS) AF: 0.975 AC: 5028 AN: 5158

South Asian (SAS) AF: 0.705 AC: 3392 AN: 4812

European-Finnish (FIN) AF: 0.473 AC: 4984 AN: 10544

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

European-Non Finnish (NFE) AF: 0.493 AC: 33475 AN: 67944

Other (OTH) AF: 0.480 AC: 1009 AN: 2104

Alfa AF: 0.452 Hom.: 10934

Bravo AF: 0.455

Asia WGS AF: 0.703 AC: 2440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.24
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs1538956; hg19: chr6-126964026; COSMIC: COSV69095951;