rs1493881

Variant names:

• chr16-65877274-G-A
• rs1493881

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;