rs2517892

Positions:

• chr6-29833697-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 0.387 in 151,938 control chromosomes in the GnomAD database, including 12,366 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 0.39 (12366 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 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: 0.387 AC: 58706 AN: 151820 Hom.: 12339 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.387 AC: 58786 AN: 151938 Hom.: 12366 Cov.: 32 AF XY: 0.389 AC XY: 28866 AN XY: 74260

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.372

Gnomad4 EAS AF: 0.513

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.289

Gnomad4 OTH AF: 0.418

Alfa AF: 0.316 Hom.: 3085

Bravo AF: 0.408

Asia WGS AF: 0.585 AC: 2029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	3.2
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517892; hg19: chr6-29801474;