rs10486788

Variant names:

• chr7-15975716-G-C
• rs10486788

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 0.239 in 152,010 control chromosomes in the GnomAD database, including 4,969 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 0.24 (4969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.239 AC: 36368 AN: 151892 Hom.: 4972 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.239 AC: 36372 AN: 152010 Hom.: 4969 Cov.: 32 AF XY: 0.245 AC XY: 18195 AN XY: 74296

African (AFR) AF: 0.116 AC: 4826 AN: 41502

American (AMR) AF: 0.319 AC: 4859 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 660 AN: 3462

East Asian (EAS) AF: 0.390 AC: 2018 AN: 5168

South Asian (SAS) AF: 0.256 AC: 1235 AN: 4824

European-Finnish (FIN) AF: 0.316 AC: 3333 AN: 10554

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18640 AN: 67934

Other (OTH) AF: 0.239 AC: 506 AN: 2114

Alfa AF: 0.248 Hom.: 605

Bravo AF: 0.236

Asia WGS AF: 0.290 AC: 1009 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.73
DANN	Benign	0.53
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs10486788; hg19: chr7-16015341;