6-139517282-C-A

Variant names:

• chr6-139517282-C-A
• rs628751
• ENST00000647815.1:n.134+30667C>A

Variant summary

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

The ENST00000647815.1(ENSG00000226571):​n.134+30667C>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 151,944 control chromosomes in the GnomAD database, including 14,785 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 (14785 hom., cov: 32)
• Consequence: ENSG00000226571 ENST00000647815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 29 publications found

Genes affected

ENSG00000226571 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647815.1. 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
	ENSG00000226571	ENST00000647815.1		n.134+30667C>A		intron	N/A
	ENSG00000226571	ENST00000775574.1		n.194-29960C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62464 AN: 151828 Hom.: 14771 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.560

Gnomad AMR AF: 0.483

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: 62488 AN: 151944 Hom.: 14785 Cov.: 32 AF XY: 0.413 AC XY: 30659 AN XY: 74250

African (AFR) AF: 0.168 AC: 6956 AN: 41412

American (AMR) AF: 0.484 AC: 7386 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.537 AC: 1863 AN: 3470

East Asian (EAS) AF: 0.271 AC: 1400 AN: 5170

South Asian (SAS) AF: 0.653 AC: 3148 AN: 4824

European-Finnish (FIN) AF: 0.453 AC: 4766 AN: 10522

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35405 AN: 67962

Other (OTH) AF: 0.432 AC: 913 AN: 2112

Alfa AF: 0.466 Hom.: 34712

Bravo AF: 0.396

Asia WGS AF: 0.469 AC: 1628 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.0
DANN	Benign	0.68
PhyloP100		-1.2

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: rs628751;

hg19: chr6-139838419;

COSMIC: COSV69428627;