rs10251680

Variant names:

• chr7-80969442-A-C
• rs10251680

Your query was ambiguous. Multiple possible variants found:

• chr7-80969442-A-C
• chr7-80969442-A-T

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 0.454 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
• 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 = 0.536 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: 0.454 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

African (AFR) AF: 0.361 AC: 14906 AN: 41288

American (AMR) AF: 0.546 AC: 8306 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1978 AN: 3464

East Asian (EAS) AF: 0.228 AC: 1171 AN: 5146

South Asian (SAS) AF: 0.514 AC: 2471 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4288 AN: 10476

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34034 AN: 67842

Other (OTH) AF: 0.483 AC: 1015 AN: 2100

Alfa AF: 0.373 Hom.: 1375

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
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs10251680; hg19: chr7-80598758;