rs10514540

Variant names:

• chr16-82448760-G-A
• rs10514540

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 0.0459 in 152,136 control chromosomes in the GnomAD database, including 229 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 0.046 (229 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.131 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: 0.0459 AC: 6976 AN: 152018 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0652

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0544

Gnomad ASJ AF: 0.0168

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.0897

Gnomad FIN AF: 0.0553

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0229

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0459 AC: 6987 AN: 152136 Hom.: 229 Cov.: 32 AF XY: 0.0488 AC XY: 3627 AN XY: 74354

African (AFR) AF: 0.0655 AC: 2716 AN: 41494

American (AMR) AF: 0.0544 AC: 832 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0168 AC: 58 AN: 3462

East Asian (EAS) AF: 0.139 AC: 718 AN: 5164

South Asian (SAS) AF: 0.0890 AC: 429 AN: 4822

European-Finnish (FIN) AF: 0.0553 AC: 585 AN: 10572

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0229 AC: 1555 AN: 68004

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0294 Hom.: 177

Bravo AF: 0.0453

Asia WGS AF: 0.109 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.2
DANN	Benign	0.72
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10514540; hg19: chr16-82482365;