rs10514473

Variant names:

• chr16-79938411-C-G
• rs10514473

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 0.112 in 152,040 control chromosomes in the GnomAD database, including 1,023 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 0.11 (1023 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.123 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: 0.112 AC: 17032 AN: 151922 Hom.: 1018 Cov.: 31

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0971

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.112 AC: 17069 AN: 152040 Hom.: 1023 Cov.: 31 AF XY: 0.112 AC XY: 8317 AN XY: 74324

African (AFR) AF: 0.0917 AC: 3804 AN: 41486

American (AMR) AF: 0.0969 AC: 1479 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3466

East Asian (EAS) AF: 0.115 AC: 594 AN: 5164

South Asian (SAS) AF: 0.118 AC: 570 AN: 4820

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8483 AN: 67956

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.116 Hom.: 113

Bravo AF: 0.111

Asia WGS AF: 0.136 AC: 474 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.75
DANN	Benign	0.63
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs10514473; hg19: chr16-79972308;