22-37431160-C-T

Variant names:

• chr22-37431160-C-T
• rs133710

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 0.326 in 151,954 control chromosomes in the GnomAD database, including 9,836 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 0.33 (9836 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.326 AC: 49558 AN: 151836 Hom.: 9836 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.476

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.326 AC: 49555 AN: 151954 Hom.: 9836 Cov.: 31 AF XY: 0.324 AC XY: 24055 AN XY: 74274

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.352

Alfa AF: 0.425 Hom.: 15734

Bravo AF: 0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs133710; hg19: chr22-37827196;