rs10486339

Variant names:

• chr7-19202357-T-A
• rs10486339

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 0.133 in 151,926 control chromosomes in the GnomAD database, including 3,097 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 0.13 (3097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.48
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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: 0.133 AC: 20233 AN: 151808 Hom.: 3088 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0746

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0417

Gnomad FIN AF: 0.0392

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0227

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.133 AC: 20275 AN: 151926 Hom.: 3097 Cov.: 32 AF XY: 0.131 AC XY: 9719 AN XY: 74258

African (AFR) AF: 0.374 AC: 15494 AN: 41376

American (AMR) AF: 0.0746 AC: 1138 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 366 AN: 3468

East Asian (EAS) AF: 0.166 AC: 857 AN: 5172

South Asian (SAS) AF: 0.0409 AC: 197 AN: 4820

European-Finnish (FIN) AF: 0.0392 AC: 415 AN: 10600

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.0227 AC: 1541 AN: 67926

Other (OTH) AF: 0.105 AC: 221 AN: 2112

Alfa AF: 0.0881 Hom.: 236

Bravo AF: 0.148

Asia WGS AF: 0.105 AC: 365 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.6
DANN	Benign	0.37
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10486339; hg19: chr7-19241980;