rs2235356

chr22-50271920-G-Achr22-50271920-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.414 in 151,604 control chromosomes in the GnomAD database, including 13,620 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 0.41 (13620 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.414 AC: 62719 AN: 151498 Hom.: 13618 Cov.: 30

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.362

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.414 AC: 62729 AN: 151604 Hom.: 13620 Cov.: 30 AF XY: 0.412 AC XY: 30546 AN XY: 74070

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.421

Alfa AF: 0.161 Hom.: 244

Bravo AF: 0.400

Asia WGS AF: 0.461 AC: 1589 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
Cadd	Benign	6.5
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235356; hg19: chr22-50710349;