rs493340

chr6-93047166-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;