rs16933964

Positions:

• chr10-76864549-A-G

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 0.0744 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0384

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0547 Hom.: 36

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16933964; hg19: chr10-78624307;