rs1512867

Positions:

• chr17-52984354-G-T

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 0.415 in 151,962 control chromosomes in the GnomAD database, including 14,029 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 0.41 (14029 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.415 AC: 63008 AN: 151842 Hom.: 14025 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.415 AC: 63048 AN: 151962 Hom.: 14029 Cov.: 32 AF XY: 0.417 AC XY: 30980 AN XY: 74274

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.225

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.423

Alfa AF: 0.457 Hom.: 2336

Bravo AF: 0.403

Asia WGS AF: 0.325 AC: 1130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1512867; hg19: chr17-51061714;