rs2493374

Positions:

• chr6-67688337-G-A
• chr6-67688337-G-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 0.476 in 151,748 control chromosomes in the GnomAD database, including 18,658 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 0.48 (18658 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.235

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.755 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72261 AN: 151632 Hom.: 18644 Cov.: 30

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.502

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.476 AC: 72298 AN: 151748 Hom.: 18658 Cov.: 30 AF XY: 0.483 AC XY: 35814 AN XY: 74120

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.775

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.587

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.506

Alfa AF: 0.503 Hom.: 2786

Bravo AF: 0.467

Asia WGS AF: 0.639 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2493374; hg19: chr6-68398230;