rs6437523

Variant names:

• chr3-104570620-C-T
• rs6437523

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 0.177 in 152,052 control chromosomes in the GnomAD database, including 2,800 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 0.18 (2800 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26938 AN: 151934 Hom.: 2802 Cov.: 32

Gnomad AFR AF: 0.0841

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.00251

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.177 AC: 26932 AN: 152052 Hom.: 2800 Cov.: 32 AF XY: 0.179 AC XY: 13312 AN XY: 74314

African (AFR) AF: 0.0840 AC: 3488 AN: 41522

American (AMR) AF: 0.211 AC: 3213 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3470

East Asian (EAS) AF: 0.00251 AC: 13 AN: 5174

South Asian (SAS) AF: 0.153 AC: 736 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2823 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15234 AN: 67932

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.210 Hom.: 10515

Bravo AF: 0.167

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.0
DANN	Benign	0.63
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6437523; hg19: chr3-104289464;