rs7089102

Variant names:

• chr10-56086406-C-A
• rs7089102

Your query was ambiguous. Multiple possible variants found:

• chr10-56086406-C-A
• chr10-56086406-C-G
• chr10-56086406-C-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 0.516 in 151,808 control chromosomes in the GnomAD database, including 20,440 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 0.52 (20440 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.419
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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: 0.516 AC: 78289 AN: 151690 Hom.: 20435 Cov.: 31

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.506

Gnomad OTH AF: 0.527

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

GnomAD4 genome AF: 0.516 AC: 78325 AN: 151808 Hom.: 20440 Cov.: 31 AF XY: 0.514 AC XY: 38169 AN XY: 74192

African (AFR) AF: 0.511 AC: 21163 AN: 41390

American (AMR) AF: 0.522 AC: 7951 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1825 AN: 3470

East Asian (EAS) AF: 0.771 AC: 3966 AN: 5144

South Asian (SAS) AF: 0.522 AC: 2517 AN: 4822

European-Finnish (FIN) AF: 0.457 AC: 4800 AN: 10512

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.506 AC: 34379 AN: 67910

Other (OTH) AF: 0.530 AC: 1117 AN: 2108

Alfa AF: 0.497 Hom.: 2462

Bravo AF: 0.519

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.64
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs7089102; hg19: chr10-57846167;