3-22574738-A-G

Variant names:

• chr3-22574738-A-G
• rs12633771

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 0.436 in 152,036 control chromosomes in the GnomAD database, including 16,679 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 0.44 (16679 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 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: 0.436 AC: 66270 AN: 151918 Hom.: 16674 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.441

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.436 AC: 66282 AN: 152036 Hom.: 16679 Cov.: 32 AF XY: 0.439 AC XY: 32587 AN XY: 74304

African (AFR) AF: 0.160 AC: 6626 AN: 41522

American (AMR) AF: 0.532 AC: 8131 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1900 AN: 3468

East Asian (EAS) AF: 0.441 AC: 2279 AN: 5166

South Asian (SAS) AF: 0.596 AC: 2877 AN: 4824

European-Finnish (FIN) AF: 0.544 AC: 5736 AN: 10544

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.544 AC: 36963 AN: 67928

Other (OTH) AF: 0.474 AC: 999 AN: 2106

Alfa AF: 0.519 Hom.: 85513

Bravo AF: 0.424

Asia WGS AF: 0.499 AC: 1739 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.73
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs12633771; hg19: chr3-22616229;