rs1493881

Positions:

• chr16-65877274-G-A
• chr16-65877274-G-C
• chr16-65877274-G-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 0.0864 in 152,182 control chromosomes in the GnomAD database, including 1,167 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 0.086 (1167 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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: 0.0864 AC: 13136 AN: 152064 Hom.: 1169 Cov.: 33

Gnomad AFR AF: 0.0607

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0769

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0526

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0864 AC: 13149 AN: 152182 Hom.: 1167 Cov.: 33 AF XY: 0.0911 AC XY: 6775 AN XY: 74400

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0769

Gnomad4 NFE AF: 0.0526

Gnomad4 OTH AF: 0.0888

Alfa AF: 0.0554 Hom.: 153

Bravo AF: 0.0946

Asia WGS AF: 0.279 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.083
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1493881; hg19: chr16-65911177;