rs7322222

Variant names:

• chr13-97482907-T-C
• rs7322222

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 0.639 in 151,952 control chromosomes in the GnomAD database, including 32,680 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 0.64 (32680 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.88
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.732 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: 0.640 AC: 97111 AN: 151834 Hom.: 32674 Cov.: 31

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.639 AC: 97152 AN: 151952 Hom.: 32680 Cov.: 31 AF XY: 0.640 AC XY: 47505 AN XY: 74252

African (AFR) AF: 0.433 AC: 17941 AN: 41428

American (AMR) AF: 0.708 AC: 10794 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2711 AN: 3472

East Asian (EAS) AF: 0.417 AC: 2153 AN: 5158

South Asian (SAS) AF: 0.745 AC: 3587 AN: 4816

European-Finnish (FIN) AF: 0.698 AC: 7362 AN: 10540

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50090 AN: 67964

Other (OTH) AF: 0.690 AC: 1458 AN: 2112

Alfa AF: 0.731 Hom.: 26382

Bravo AF: 0.629

Asia WGS AF: 0.572 AC: 1989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.072
DANN	Benign	0.24
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs7322222; hg19: chr13-98135161;