6-52250815-C-T

Variant names:

• chr6-52250815-C-T
• rs3857604

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 0.258 in 149,350 control chromosomes in the GnomAD database, including 5,633 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 0.26 (5633 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.09
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.258 AC: 38482 AN: 149240 Hom.: 5624 Cov.: 31

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.258 AC: 38523 AN: 149350 Hom.: 5633 Cov.: 31 AF XY: 0.260 AC XY: 18955 AN XY: 72840

African (AFR) AF: 0.400 AC: 16308 AN: 40784

American (AMR) AF: 0.189 AC: 2837 AN: 15040

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 796 AN: 3442

East Asian (EAS) AF: 0.319 AC: 1621 AN: 5086

South Asian (SAS) AF: 0.226 AC: 1052 AN: 4646

European-Finnish (FIN) AF: 0.241 AC: 2426 AN: 10082

Middle Eastern (MID) AF: 0.240 AC: 69 AN: 288

European-Non Finnish (NFE) AF: 0.189 AC: 12672 AN: 67018

Other (OTH) AF: 0.239 AC: 494 AN: 2068

Alfa AF: 0.278 Hom.: 2621

Bravo AF: 0.259

Asia WGS AF: 0.262 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.36
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs3857604; hg19: chr6-52115613;