rs16933964

Variant names:

• chr10-76864549-A-G
• rs16933964

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 0.0744 in 152,170 control chromosomes in the GnomAD database, including 516 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 0.074 (516 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 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: 0.0743 AC: 11304 AN: 152052 Hom.: 514 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0707

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0384

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0744 AC: 11321 AN: 152170 Hom.: 516 Cov.: 32 AF XY: 0.0782 AC XY: 5818 AN XY: 74402

African (AFR) AF: 0.128 AC: 5318 AN: 41526

American (AMR) AF: 0.0707 AC: 1082 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3468

East Asian (EAS) AF: 0.116 AC: 599 AN: 5176

South Asian (SAS) AF: 0.159 AC: 768 AN: 4816

European-Finnish (FIN) AF: 0.0626 AC: 662 AN: 10582

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0384 AC: 2609 AN: 67986

Other (OTH) AF: 0.0629 AC: 133 AN: 2114

Alfa AF: 0.0568 Hom.: 41

Bravo AF: 0.0743

Asia WGS AF: 0.142 AC: 489 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.31
DANN	Benign	0.44
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs16933964; hg19: chr10-78624307;