rs1493902

Positions:

• chr16-54695774-C-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 0.671 in 152,104 control chromosomes in the GnomAD database, including 35,849 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 0.67 (35849 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.784 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: 0.671 AC: 101994 AN: 151986 Hom.: 35850 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.789

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.671 AC: 102017 AN: 152104 Hom.: 35849 Cov.: 33 AF XY: 0.669 AC XY: 49733 AN XY: 74358

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.789

Gnomad4 OTH AF: 0.649

Alfa AF: 0.731 Hom.: 10302

Bravo AF: 0.646

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493902; hg19: chr16-54729686;