chr6-139421651-G-A

Variant names:

• chr6-139421651-G-A
• rs887780
• ENST00000650173.1:n.510-7430G>A

Variant summary

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

The ENST00000650173.1(ENSG00000226571):​n.510-7430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.701 in 152,120 control chromosomes in the GnomAD database, including 37,560 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 0.70 (37560 hom., cov: 33)
• Consequence: ENSG00000226571 ENST00000650173.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 3 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650173.1. 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
	ENSG00000226571	ENST00000650173.1		n.510-7430G>A		intron	N/A
	ENSG00000226571	ENST00000775570.1		n.420-7430G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106623 AN: 152002 Hom.: 37535 Cov.: 33

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.710

Gnomad OTH AF: 0.695

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

GnomAD4 genome AF: 0.701 AC: 106712 AN: 152120 Hom.: 37560 Cov.: 33 AF XY: 0.698 AC XY: 51915 AN XY: 74356

African (AFR) AF: 0.726 AC: 30121 AN: 41510

American (AMR) AF: 0.690 AC: 10548 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3466

East Asian (EAS) AF: 0.666 AC: 3432 AN: 5154

South Asian (SAS) AF: 0.581 AC: 2801 AN: 4824

European-Finnish (FIN) AF: 0.681 AC: 7204 AN: 10576

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.710 AC: 48252 AN: 67990

Other (OTH) AF: 0.695 AC: 1470 AN: 2114

Alfa AF: 0.705 Hom.: 64797

Bravo AF: 0.706

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.20
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs887780; hg19: chr6-139742788;