rs887780

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr6-139421651-G-A
• chr6-139421651-G-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986651	XR_001744382.1	n.105+1880G>A		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226571	ENST00000650173.1	n.510-7430G>A		intron_variant	Intron 4 of 7
ENSG00000226571	ENST00000775570.1	n.420-7430G>A		intron_variant	Intron 4 of 6

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 v4.3

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;