rs10271980

Variant names:

• chr7-68880612-G-A
• rs10271980

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.588

Alfa AF: 0.594 Hom.: 27006

Bravo AF: 0.581

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10271980; hg19: chr7-68345599;