rs17878544

Positions:

• chr16-31096606-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 0.106 in 152,176 control chromosomes in the GnomAD database, including 2,646 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 0.11 (2646 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.232

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.349 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: 0.106 AC: 16125 AN: 152058 Hom.: 2637 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0497

Gnomad ASJ AF: 0.00577

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.00682

Gnomad OTH AF: 0.0842

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

GnomAD4 genome AF: 0.106 AC: 16163 AN: 152176 Hom.: 2646 Cov.: 33 AF XY: 0.102 AC XY: 7618 AN XY: 74430

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.0495

Gnomad4 ASJ AF: 0.00577

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00682

Gnomad4 OTH AF: 0.0833

Alfa AF: 0.0531 Hom.: 413

Bravo AF: 0.121

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17878544; hg19: chr16-31107927;