rs2517912

Variant names:

• chr6-29716167-C-T
• rs2517912

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 0.44 in 152,066 control chromosomes in the GnomAD database, including 14,887 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 0.44 (14887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.441 AC: 66936 AN: 151946 Hom.: 14875 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.440 AC: 66974 AN: 152066 Hom.: 14887 Cov.: 32 AF XY: 0.438 AC XY: 32532 AN XY: 74314

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.530

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.453

Alfa AF: 0.458 Hom.: 17425

Bravo AF: 0.446

Asia WGS AF: 0.321 AC: 1116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2517912; hg19: chr6-29683944;