rs2106139

Variant names:

• chr22-19577734-G-A
• rs2106139

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 0.134 in 152,168 control chromosomes in the GnomAD database, including 2,777 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 0.13 (2777 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 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: 0.134 AC: 20309 AN: 152048 Hom.: 2761 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0843

Gnomad ASJ AF: 0.0700

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0846

Gnomad FIN AF: 0.0224

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.134 AC: 20354 AN: 152168 Hom.: 2777 Cov.: 32 AF XY: 0.132 AC XY: 9820 AN XY: 74410

African (AFR) AF: 0.345 AC: 14304 AN: 41472

American (AMR) AF: 0.0845 AC: 1292 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0700 AC: 243 AN: 3472

East Asian (EAS) AF: 0.120 AC: 621 AN: 5158

South Asian (SAS) AF: 0.0845 AC: 408 AN: 4830

European-Finnish (FIN) AF: 0.0224 AC: 238 AN: 10618

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2957 AN: 68006

Other (OTH) AF: 0.118 AC: 249 AN: 2114

Alfa AF: 0.176 Hom.: 1427

Bravo AF: 0.147

Asia WGS AF: 0.110 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.69
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs2106139; hg19: chr22-19565257;