rs1493902

Variant names:

• chr16-54695774-C-T
• rs1493902

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 0.671 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.495 AC: 20526 AN: 41452

American (AMR) AF: 0.606 AC: 9258 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.737 AC: 2558 AN: 3472

East Asian (EAS) AF: 0.406 AC: 2093 AN: 5154

South Asian (SAS) AF: 0.587 AC: 2824 AN: 4808

European-Finnish (FIN) AF: 0.815 AC: 8648 AN: 10606

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.789 AC: 53687 AN: 68004

Other (OTH) AF: 0.649 AC: 1371 AN: 2114

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1493902; hg19: chr16-54729686;