22-19740662-A-G

Variant names:

• chr22-19740662-A-G
• rs2871042

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 0.461 in 152,150 control chromosomes in the GnomAD database, including 16,557 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 0.46 (16557 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.524 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: 0.462 AC: 70167 AN: 152032 Hom.: 16554 Cov.: 34

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.461 AC: 70194 AN: 152150 Hom.: 16557 Cov.: 34 AF XY: 0.465 AC XY: 34614 AN XY: 74388

African (AFR) AF: 0.395 AC: 16412 AN: 41526

American (AMR) AF: 0.534 AC: 8167 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2683 AN: 5160

South Asian (SAS) AF: 0.340 AC: 1638 AN: 4824

European-Finnish (FIN) AF: 0.540 AC: 5719 AN: 10586

Middle Eastern (MID) AF: 0.463 AC: 136 AN: 294

European-Non Finnish (NFE) AF: 0.478 AC: 32483 AN: 67974

Other (OTH) AF: 0.473 AC: 999 AN: 2112

Alfa AF: 0.475 Hom.: 2688

Bravo AF: 0.461

Asia WGS AF: 0.426 AC: 1484 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	2.6
DANN	Benign	0.36
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2871042; hg19: chr22-19728185;