rs4922522

Variant names:

• chr10-47185561-T-G
• rs4922522

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0311 in 152,192 control chromosomes in the GnomAD database, including 100 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 0.031 (100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0311 (4736/152192) while in subpopulation AFR AF = 0.0448 (1861/41532). AF 95% confidence interval is 0.0431. There are 100 homozygotes in GnomAd4. There are 2296 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 100 gene

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0311 AC: 4734 AN: 152074 Hom.: 100 Cov.: 32

Gnomad AFR AF: 0.0448

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0949

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0245

Gnomad OTH AF: 0.0462

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

GnomAD4 genome AF: 0.0311 AC: 4736 AN: 152192 Hom.: 100 Cov.: 32 AF XY: 0.0308 AC XY: 2296 AN XY: 74430

African (AFR) AF: 0.0448 AC: 1861 AN: 41532

American (AMR) AF: 0.0345 AC: 528 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0949 AC: 329 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5156

South Asian (SAS) AF: 0.0166 AC: 80 AN: 4818

European-Finnish (FIN) AF: 0.0126 AC: 134 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0245 AC: 1667 AN: 68010

Other (OTH) AF: 0.0457 AC: 96 AN: 2100

Alfa AF: 0.0269 Hom.: 42

Bravo AF: 0.0335

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.70
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4922522; hg19: chr10-48553801;