4-102167334-A-G

Variant names:

• chr4-102167334-A-G
• rs17032126

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 0.105 in 152,260 control chromosomes in the GnomAD database, including 1,199 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 (1199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0730
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16007 AN: 152140 Hom.: 1199 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.105 AC: 16012 AN: 152260 Hom.: 1199 Cov.: 32 AF XY: 0.109 AC XY: 8142 AN XY: 74442

African (AFR) AF: 0.0223 AC: 928 AN: 41578

American (AMR) AF: 0.203 AC: 3109 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1182 AN: 5172

South Asian (SAS) AF: 0.104 AC: 503 AN: 4826

European-Finnish (FIN) AF: 0.129 AC: 1373 AN: 10608

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7935 AN: 68000

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.113 Hom.: 3529

Bravo AF: 0.108

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		-0.073

Splicing

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

Other links and lift over

dbSNP: rs17032126; hg19: chr4-103088491;