22-32180380-C-T

Variant names:

• chr22-32180380-C-T
• rs136422

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 0.337 in 151,982 control chromosomes in the GnomAD database, including 9,653 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 0.34 (9653 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 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: 0.337 AC: 51162 AN: 151864 Hom.: 9629 Cov.: 31

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.337 AC: 51233 AN: 151982 Hom.: 9653 Cov.: 31 AF XY: 0.333 AC XY: 24760 AN XY: 74286

African (AFR) AF: 0.501 AC: 20747 AN: 41416

American (AMR) AF: 0.211 AC: 3231 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 977 AN: 3470

East Asian (EAS) AF: 0.0903 AC: 468 AN: 5180

South Asian (SAS) AF: 0.288 AC: 1384 AN: 4808

European-Finnish (FIN) AF: 0.279 AC: 2950 AN: 10566

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20554 AN: 67940

Other (OTH) AF: 0.295 AC: 622 AN: 2110

Alfa AF: 0.329 Hom.: 1555

Bravo AF: 0.338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.34
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs136422; hg19: chr22-32576367;