rs10483340

Variant names:

• chr14-28622631-A-C
• rs10483340

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 0.304 in 151,840 control chromosomes in the GnomAD database, including 7,283 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 0.30 (7283 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.417 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: 0.304 AC: 46072 AN: 151722 Hom.: 7265 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.278

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.304 AC: 46124 AN: 151840 Hom.: 7283 Cov.: 32 AF XY: 0.308 AC XY: 22840 AN XY: 74228

African (AFR) AF: 0.254 AC: 10512 AN: 41462

American (AMR) AF: 0.426 AC: 6476 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1331 AN: 3464

East Asian (EAS) AF: 0.355 AC: 1819 AN: 5124

South Asian (SAS) AF: 0.395 AC: 1903 AN: 4816

European-Finnish (FIN) AF: 0.278 AC: 2940 AN: 10562

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20222 AN: 67886

Other (OTH) AF: 0.326 AC: 687 AN: 2108

Alfa AF: 0.303 Hom.: 888

Bravo AF: 0.313

Asia WGS AF: 0.372 AC: 1292 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs10483340; hg19: chr14-29091837;