rs10246622

Variant names:

• chr7-97104745-A-G
• rs10246622

Your query was ambiguous. Multiple possible variants found:

• chr7-97104745-A-G
• chr7-97104745-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 0.394 in 151,994 control chromosomes in the GnomAD database, including 12,089 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 0.39 (12089 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.473 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: 0.394 AC: 59857 AN: 151876 Hom.: 12064 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.394 AC: 59931 AN: 151994 Hom.: 12089 Cov.: 32 AF XY: 0.396 AC XY: 29422 AN XY: 74278

African (AFR) AF: 0.474 AC: 19660 AN: 41436

American (AMR) AF: 0.380 AC: 5808 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1377 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2513 AN: 5138

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4818

European-Finnish (FIN) AF: 0.357 AC: 3773 AN: 10570

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23649 AN: 67974

Other (OTH) AF: 0.409 AC: 863 AN: 2110

Alfa AF: 0.364 Hom.: 3533

Bravo AF: 0.403

Asia WGS AF: 0.466 AC: 1618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.41
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10246622; hg19: chr7-96734057;