rs493340

Variant names:

• chr6-93047166-T-C
• rs493340

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 0.423 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.423 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

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.479

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.404

Alfa AF: 0.383 Hom.: 6028

Bravo AF: 0.440

Asia WGS AF: 0.319 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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