22-31042375-C-T

Variant names:

• chr22-31042375-C-T
• rs111383589

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 0.114 in 151,926 control chromosomes in the GnomAD database, including 1,114 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 0.11 (1114 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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: 0.114 AC: 17265 AN: 151810 Hom.: 1111 Cov.: 31

Gnomad AFR AF: 0.0884

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.0838

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.00234

Gnomad SAS AF: 0.0662

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.114 AC: 17286 AN: 151926 Hom.: 1114 Cov.: 31 AF XY: 0.111 AC XY: 8233 AN XY: 74268

African (AFR) AF: 0.0883 AC: 3664 AN: 41476

American (AMR) AF: 0.0838 AC: 1282 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3468

East Asian (EAS) AF: 0.00235 AC: 12 AN: 5106

South Asian (SAS) AF: 0.0664 AC: 320 AN: 4818

European-Finnish (FIN) AF: 0.140 AC: 1482 AN: 10562

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9619 AN: 67898

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.0552 Hom.: 56

Bravo AF: 0.111

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.59
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs111383589; hg19: chr22-31438361;