rs10487315

Variant names:

• chr7-109980469-G-A
• rs10487315

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 0.06 in 152,136 control chromosomes in the GnomAD database, including 586 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 0.060 (586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0598 AC: 9093 AN: 152018 Hom.: 583 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.00179

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0600 AC: 9123 AN: 152136 Hom.: 586 Cov.: 32 AF XY: 0.0584 AC XY: 4345 AN XY: 74382

African (AFR) AF: 0.144 AC: 5992 AN: 41472

American (AMR) AF: 0.0331 AC: 506 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0153 AC: 53 AN: 3458

East Asian (EAS) AF: 0.163 AC: 843 AN: 5170

South Asian (SAS) AF: 0.0617 AC: 297 AN: 4816

European-Finnish (FIN) AF: 0.00179 AC: 19 AN: 10600

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0190 AC: 1295 AN: 68010

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0422 Hom.: 48

Bravo AF: 0.0669

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs10487315; hg19: chr7-109620526;