6-52152310-T-C

Variant names:

• chr6-52152310-T-C
• rs13206743

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 0.306 in 151,840 control chromosomes in the GnomAD database, including 9,159 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 0.31 (9159 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.09
• Publications: 6 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 (NFE) allele frequency at 95% confidence interval = 0.439 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: 0.306 AC: 46422 AN: 151722 Hom.: 9162 Cov.: 30

Gnomad AFR AF: 0.0903

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0510

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.306 AC: 46413 AN: 151840 Hom.: 9159 Cov.: 30 AF XY: 0.301 AC XY: 22368 AN XY: 74226

African (AFR) AF: 0.0902 AC: 3739 AN: 41452

American (AMR) AF: 0.253 AC: 3856 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1397 AN: 3466

East Asian (EAS) AF: 0.0513 AC: 264 AN: 5146

South Asian (SAS) AF: 0.250 AC: 1202 AN: 4800

European-Finnish (FIN) AF: 0.451 AC: 4758 AN: 10542

Middle Eastern (MID) AF: 0.255 AC: 74 AN: 290

European-Non Finnish (NFE) AF: 0.443 AC: 30097 AN: 67870

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.238 Hom.: 1009

Bravo AF: 0.281

Asia WGS AF: 0.156 AC: 547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.013
DANN	Benign	0.75
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs13206743; hg19: chr6-52017108;