rs493340

Variant names:

• chr6-93047166-T-C
• rs493340

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 0.423 in 152,044 control chromosomes in the GnomAD database, including 14,173 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 0.42 (14173 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64306 AN: 151926 Hom.: 14155 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.423 AC: 64361 AN: 152044 Hom.: 14173 Cov.: 32 AF XY: 0.422 AC XY: 31360 AN XY: 74322

African (AFR) AF: 0.545 AC: 22607 AN: 41444

American (AMR) AF: 0.479 AC: 7307 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5162

South Asian (SAS) AF: 0.371 AC: 1791 AN: 4822

European-Finnish (FIN) AF: 0.344 AC: 3642 AN: 10574

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25048 AN: 67978

Other (OTH) AF: 0.404 AC: 855 AN: 2116

Alfa AF: 0.382 Hom.: 6569

Bravo AF: 0.440

Asia WGS AF: 0.319 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.78
DANN	Benign	0.67
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs493340; hg19: chr6-93756884; COSMIC: COSV60247572;