rs10488559

Variant names:

• chr7-52047099-A-G
• rs10488559

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 0.0322 in 152,306 control chromosomes in the GnomAD database, including 100 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 0.032 (100 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0322 (4905/152306) while in subpopulation NFE AF = 0.0478 (3248/68020). AF 95% confidence interval is 0.0464. There are 100 homozygotes in GnomAd4. There are 2369 alleles in the male GnomAd4 subpopulation. Median coverage is 34. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 100 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: 0.0322 AC: 4905 AN: 152188 Hom.: 101 Cov.: 34

Gnomad AFR AF: 0.00823

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0393

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0477

Gnomad OTH AF: 0.0359

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

GnomAD4 genome AF: 0.0322 AC: 4905 AN: 152306 Hom.: 100 Cov.: 34 AF XY: 0.0318 AC XY: 2369 AN XY: 74472

African (AFR) AF: 0.00820 AC: 341 AN: 41578

American (AMR) AF: 0.0262 AC: 400 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0398 AC: 192 AN: 4826

European-Finnish (FIN) AF: 0.0491 AC: 521 AN: 10618

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0478 AC: 3248 AN: 68020

Other (OTH) AF: 0.0355 AC: 75 AN: 2110

Alfa AF: 0.0424 Hom.: 45

Bravo AF: 0.0292

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	2.4
DANN	Benign	0.80
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs10488559; hg19: chr7-52114795;