22-31957907-G-T

Variant names:

• chr22-31957907-G-T
• rs2853887

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 0.24 in 152,062 control chromosomes in the GnomAD database, including 5,408 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 0.24 (5408 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36469 AN: 151944 Hom.: 5401 Cov.: 32

Gnomad AFR AF: 0.0720

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.240 AC: 36487 AN: 152062 Hom.: 5408 Cov.: 32 AF XY: 0.242 AC XY: 17978 AN XY: 74322

African (AFR) AF: 0.0719 AC: 2983 AN: 41488

American (AMR) AF: 0.302 AC: 4612 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1165 AN: 3468

East Asian (EAS) AF: 0.141 AC: 728 AN: 5170

South Asian (SAS) AF: 0.282 AC: 1356 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3155 AN: 10570

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21574 AN: 67960

Other (OTH) AF: 0.258 AC: 544 AN: 2112

Alfa AF: 0.165 Hom.: 390

Bravo AF: 0.230

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.67
PhyloP100		-0.077

Splicing

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

Other links and lift over

dbSNP: rs2853887; hg19: chr22-32353894;