rs6437523

Positions:

• chr3-104570620-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0840

Gnomad4 AMR AF: 0.211

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.153

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.199

Alfa AF: 0.216 Hom.: 7365

Bravo AF: 0.167

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6437523; hg19: chr3-104289464;