rs7896131

Variant names:

• chr10-92789918-G-A
• rs7896131

Your query was ambiguous. Multiple possible variants found:

• chr10-92789918-G-A
• chr10-92789918-G-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 0.82 in 152,168 control chromosomes in the GnomAD database, including 51,372 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 0.82 (51372 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 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: 0.820 AC: 124730 AN: 152048 Hom.: 51325 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.819

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

GnomAD4 genome AF: 0.820 AC: 124838 AN: 152168 Hom.: 51372 Cov.: 32 AF XY: 0.823 AC XY: 61229 AN XY: 74384

African (AFR) AF: 0.809 AC: 33577 AN: 41504

American (AMR) AF: 0.861 AC: 13165 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.817 AC: 2835 AN: 3470

East Asian (EAS) AF: 0.971 AC: 5034 AN: 5182

South Asian (SAS) AF: 0.928 AC: 4479 AN: 4826

European-Finnish (FIN) AF: 0.788 AC: 8336 AN: 10574

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54679 AN: 68002

Other (OTH) AF: 0.820 AC: 1734 AN: 2114

Alfa AF: 0.812 Hom.: 20647

Bravo AF: 0.826

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	18
DANN	Benign	0.59
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs7896131; hg19: chr10-94549675;