4-102095704-G-T

Variant names:

• chr4-102095704-G-T
• rs12641017

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 0.0364 in 152,274 control chromosomes in the GnomAD database, including 156 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 0.036 (156 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.531
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0744 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: 0.0364 AC: 5537 AN: 152156 Hom.: 154 Cov.: 33

Gnomad AFR AF: 0.0132

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0666

Gnomad EAS AF: 0.0806

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.0240

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0331

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

GnomAD4 genome AF: 0.0364 AC: 5538 AN: 152274 Hom.: 156 Cov.: 33 AF XY: 0.0365 AC XY: 2716 AN XY: 74460

African (AFR) AF: 0.0132 AC: 547 AN: 41558

American (AMR) AF: 0.0369 AC: 565 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0666 AC: 231 AN: 3470

East Asian (EAS) AF: 0.0808 AC: 418 AN: 5176

South Asian (SAS) AF: 0.0553 AC: 267 AN: 4824

European-Finnish (FIN) AF: 0.0240 AC: 255 AN: 10608

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0455 AC: 3098 AN: 68026

Other (OTH) AF: 0.0365 AC: 77 AN: 2108

Alfa AF: 0.0364 Hom.: 59

Bravo AF: 0.0363

Asia WGS AF: 0.0860 AC: 298 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.026
DANN	Benign	0.73
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs12641017; hg19: chr4-103016861;