rs6531493

Variant names:

• chr4-36915333-G-T
• rs6531493

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 0.352 in 151,906 control chromosomes in the GnomAD database, including 10,186 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 0.35 (10186 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.453 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: 0.352 AC: 53395 AN: 151790 Hom.: 10158 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.352 AC: 53467 AN: 151906 Hom.: 10186 Cov.: 32 AF XY: 0.347 AC XY: 25775 AN XY: 74236

African (AFR) AF: 0.459 AC: 18982 AN: 41388

American (AMR) AF: 0.257 AC: 3924 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1271 AN: 3454

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5188

South Asian (SAS) AF: 0.152 AC: 732 AN: 4826

European-Finnish (FIN) AF: 0.382 AC: 4024 AN: 10534

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23359 AN: 67934

Other (OTH) AF: 0.351 AC: 740 AN: 2108

Alfa AF: 0.340 Hom.: 38886

Bravo AF: 0.349

Asia WGS AF: 0.126 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.27
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs6531493; hg19: chr4-36916955;