17-51152947-T-C

Variant names:

• chr17-51152947-T-C
• rs16949649

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 0.386 in 151,952 control chromosomes in the GnomAD database, including 11,324 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 (11324 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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: 0.386 AC: 58626 AN: 151834 Hom.: 11310 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58677 AN: 151952 Hom.: 11324 Cov.: 31 AF XY: 0.382 AC XY: 28386 AN XY: 74288

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.409

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.396

Gnomad4 OTH AF: 0.400

Alfa AF: 0.400 Hom.: 1095

Bravo AF: 0.391

Asia WGS AF: 0.362 AC: 1259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16949649; hg19: chr17-49230308;