17-51152947-T-C

Variant names:

• chr17-51152947-T-C
• rs16949649

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 47 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.375 AC: 15522 AN: 41424

American (AMR) AF: 0.406 AC: 6197 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1416 AN: 3464

East Asian (EAS) AF: 0.382 AC: 1977 AN: 5174

South Asian (SAS) AF: 0.309 AC: 1491 AN: 4820

European-Finnish (FIN) AF: 0.362 AC: 3827 AN: 10562

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26915 AN: 67940

Other (OTH) AF: 0.400 AC: 844 AN: 2112

Alfa AF: 0.394 Hom.: 39236

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
PhyloP100		-0.041

Splicing

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

Other links and lift over

dbSNP: rs16949649; hg19: chr17-49230308;