rs62236673

Variant names:

• chr22-37680056-G-A
• rs62236673

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 0.302 in 152,118 control chromosomes in the GnomAD database, including 7,200 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 0.30 (7200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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: 0.303 AC: 45989 AN: 152000 Hom.: 7209 Cov.: 33

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.302 AC: 45981 AN: 152118 Hom.: 7200 Cov.: 33 AF XY: 0.301 AC XY: 22377 AN XY: 74360

African (AFR) AF: 0.222 AC: 9204 AN: 41510

American (AMR) AF: 0.302 AC: 4613 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3466

East Asian (EAS) AF: 0.261 AC: 1348 AN: 5168

South Asian (SAS) AF: 0.272 AC: 1312 AN: 4824

European-Finnish (FIN) AF: 0.321 AC: 3392 AN: 10578

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23485 AN: 67984

Other (OTH) AF: 0.319 AC: 672 AN: 2108

Alfa AF: 0.336 Hom.: 2898

Bravo AF: 0.297

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.7
DANN	Benign	0.63
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs62236673; hg19: chr22-38076063;