chr4-18964311-C-T

Variant names:

• chr4-18964311-C-T
• rs2537934

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 0.117 in 151,820 control chromosomes in the GnomAD database, including 1,727 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 0.12 (1727 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.263 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: 0.116 AC: 17660 AN: 151696 Hom.: 1715 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0591

Gnomad EAS AF: 0.0428

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0267

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0560

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.117 AC: 17702 AN: 151820 Hom.: 1727 Cov.: 32 AF XY: 0.115 AC XY: 8525 AN XY: 74176

African (AFR) AF: 0.268 AC: 11083 AN: 41406

American (AMR) AF: 0.0701 AC: 1067 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.0591 AC: 205 AN: 3468

East Asian (EAS) AF: 0.0431 AC: 223 AN: 5170

South Asian (SAS) AF: 0.152 AC: 729 AN: 4806

European-Finnish (FIN) AF: 0.0267 AC: 281 AN: 10524

Middle Eastern (MID) AF: 0.135 AC: 39 AN: 288

European-Non Finnish (NFE) AF: 0.0560 AC: 3800 AN: 67908

Other (OTH) AF: 0.121 AC: 255 AN: 2108

Alfa AF: 0.0902 Hom.: 148

Bravo AF: 0.124

Asia WGS AF: 0.0950 AC: 328 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.15
PhyloP100		0.025

Splicing

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

Other links and lift over

dbSNP: rs2537934; hg19: chr4-18965934;