rs10486338

Variant names:

• chr7-19169582-G-A
• rs10486338

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0285 in 152,088 control chromosomes in the GnomAD database, including 103 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 0.029 (103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0285 (4336/152088) while in subpopulation NFE AF = 0.0408 (2775/67972). AF 95% confidence interval is 0.0396. There are 103 homozygotes in GnomAd4. There are 2171 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 103 gene

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: 0.0285 AC: 4338 AN: 151970 Hom.: 103 Cov.: 32

Gnomad AFR AF: 0.00546

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0125

Gnomad FIN AF: 0.0726

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0285 AC: 4336 AN: 152088 Hom.: 103 Cov.: 32 AF XY: 0.0292 AC XY: 2171 AN XY: 74348

African (AFR) AF: 0.00544 AC: 226 AN: 41512

American (AMR) AF: 0.0194 AC: 296 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5168

South Asian (SAS) AF: 0.0125 AC: 60 AN: 4812

European-Finnish (FIN) AF: 0.0726 AC: 768 AN: 10582

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0408 AC: 2775 AN: 67972

Other (OTH) AF: 0.0321 AC: 68 AN: 2116

Alfa AF: 0.0450 Hom.: 31

Bravo AF: 0.0232

Asia WGS AF: 0.00866 AC: 31 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.77
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10486338; hg19: chr7-19209205;