6-126484109-A-G

Variant names:

• chr6-126484109-A-G
• rs2050644
• ENST00000651326.1:n.2290-11515T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000651326.1(ENSG00000293110):​n.2290-11515T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,616 control chromosomes in the GnomAD database, including 16,418 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 0.43 (16418 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000651326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.436
• Publications: 17 publications found

Genes affected

ENSG00000293110 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.43).
• 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: ENST00000651326.1. 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	ENST00000651326.1		n.2290-11515T>C		intron	N/A
	ENSG00000293110	ENST00000652383.1		n.630+47554T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65391 AN: 151498 Hom.: 16417 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.431 AC: 65394 AN: 151616 Hom.: 16418 Cov.: 32 AF XY: 0.442 AC XY: 32732 AN XY: 74130

African (AFR) AF: 0.210 AC: 8711 AN: 41444

American (AMR) AF: 0.609 AC: 9280 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3464

East Asian (EAS) AF: 0.975 AC: 5046 AN: 5176

South Asian (SAS) AF: 0.672 AC: 3235 AN: 4812

European-Finnish (FIN) AF: 0.436 AC: 4515 AN: 10352

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31330 AN: 67830

Other (OTH) AF: 0.463 AC: 976 AN: 2106

Alfa AF: 0.342 Hom.: 2549

Bravo AF: 0.437

Asia WGS AF: 0.692 AC: 2368 AN: 3430

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.43
CADD	Benign	4.2
DANN	Benign	0.97
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2050644; hg19: chr6-126805255; COSMIC: COSV66037164;