rs10251680

chr7-80969442-A-Cchr7-80969442-A-T

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 0.454 in 151,542 control chromosomes in the GnomAD database, including 16,217 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 0.45 (16217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.799

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 = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68721 AN: 151426 Hom.: 16208 Cov.: 30

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.545

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.454 AC: 68767 AN: 151542 Hom.: 16217 Cov.: 30 AF XY: 0.450 AC XY: 33265 AN XY: 73994

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.546

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.228

Gnomad4 SAS AF: 0.514

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.502

Gnomad4 OTH AF: 0.483

Alfa AF: 0.374 Hom.: 1320

Bravo AF: 0.458

Asia WGS AF: 0.399 AC: 1385 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.60
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10251680; hg19: chr7-80598758;