rs4922522

Positions:

• chr10-47185561-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 100 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.0345

Gnomad4 ASJ AF: 0.0949

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.0126

Gnomad4 NFE AF: 0.0245

Gnomad4 OTH AF: 0.0457

Alfa AF: 0.0266 Hom.: 39

Bravo AF: 0.0335

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4922522; hg19: chr10-48553801;