rs1861760

Variant names:

• chr16-50823782-A-C
• rs1861760

Your query was ambiguous. Multiple possible variants found:

• chr16-50823782-A-C
• chr16-50823782-A-T

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 0.91 in 152,236 control chromosomes in the GnomAD database, including 63,415 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 0.91 (63415 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.951 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: 0.910 AC: 138484 AN: 152120 Hom.: 63379 Cov.: 33

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.945

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.949

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.958

Gnomad OTH AF: 0.910

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

GnomAD4 genome AF: 0.910 AC: 138578 AN: 152236 Hom.: 63415 Cov.: 33 AF XY: 0.907 AC XY: 67517 AN XY: 74426

African (AFR) AF: 0.835 AC: 34657 AN: 41506

American (AMR) AF: 0.945 AC: 14462 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.963 AC: 3341 AN: 3470

East Asian (EAS) AF: 0.861 AC: 4460 AN: 5182

South Asian (SAS) AF: 0.697 AC: 3358 AN: 4816

European-Finnish (FIN) AF: 0.949 AC: 10068 AN: 10612

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.958 AC: 65151 AN: 68032

Other (OTH) AF: 0.910 AC: 1921 AN: 2112

Alfa AF: 0.940 Hom.: 192059

Bravo AF: 0.911

Asia WGS AF: 0.795 AC: 2767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.74
DANN	Benign	0.64
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1861760; hg19: chr16-50857693;