rs10271980

Variant names:

• chr7-68880612-G-A
• rs10271980

Variant summary

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

The variant allele was found at a frequency of 0.576 in 152,004 control chromosomes in the GnomAD database, including 25,559 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 0.58 (25559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 1 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87569 AN: 151888 Hom.: 25545 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.576 AC: 87627 AN: 152004 Hom.: 25559 Cov.: 32 AF XY: 0.577 AC XY: 42900 AN XY: 74288

African (AFR) AF: 0.523 AC: 21678 AN: 41470

American (AMR) AF: 0.662 AC: 10108 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1951 AN: 3468

East Asian (EAS) AF: 0.607 AC: 3114 AN: 5134

South Asian (SAS) AF: 0.558 AC: 2690 AN: 4818

European-Finnish (FIN) AF: 0.586 AC: 6187 AN: 10566

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.589 AC: 40007 AN: 67960

Other (OTH) AF: 0.588 AC: 1242 AN: 2114

Alfa AF: 0.592 Hom.: 35000

Bravo AF: 0.581

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.42
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10271980; hg19: chr7-68345599;