rs1103775

Variant names:

• chr16-65932526-G-A
• rs1103775

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 0.679 in 152,164 control chromosomes in the GnomAD database, including 35,917 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 0.68 (35917 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.84 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: 0.679 AC: 103237 AN: 152046 Hom.: 35876 Cov.: 33

Gnomad AFR AF: 0.847

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.595

Gnomad OTH AF: 0.642

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

GnomAD4 genome AF: 0.679 AC: 103328 AN: 152164 Hom.: 35917 Cov.: 33 AF XY: 0.678 AC XY: 50435 AN XY: 74384

African (AFR) AF: 0.847 AC: 35190 AN: 41534

American (AMR) AF: 0.647 AC: 9891 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2212 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3637 AN: 5170

South Asian (SAS) AF: 0.637 AC: 3071 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6755 AN: 10570

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.595 AC: 40461 AN: 67994

Other (OTH) AF: 0.637 AC: 1343 AN: 2108

Alfa AF: 0.648 Hom.: 13003

Bravo AF: 0.690

Asia WGS AF: 0.671 AC: 2332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.62
PhyloP100		-0.074

Splicing

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

Other links and lift over

dbSNP: rs1103775; hg19: chr16-65966429;