rs10245560

Variant names:

• chr7-129559487-G-A
• rs10245560

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 0.343 in 152,010 control chromosomes in the GnomAD database, including 10,011 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 0.34 (10011 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 5 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 (NFE) allele frequency at 95% confidence interval = 0.439 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: 0.343 AC: 52156 AN: 151892 Hom.: 10009 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.00963

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.343 AC: 52173 AN: 152010 Hom.: 10011 Cov.: 32 AF XY: 0.337 AC XY: 25050 AN XY: 74294

African (AFR) AF: 0.230 AC: 9532 AN: 41434

American (AMR) AF: 0.282 AC: 4308 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1452 AN: 3470

East Asian (EAS) AF: 0.00965 AC: 50 AN: 5180

South Asian (SAS) AF: 0.238 AC: 1147 AN: 4824

European-Finnish (FIN) AF: 0.403 AC: 4250 AN: 10542

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30116 AN: 67972

Other (OTH) AF: 0.350 AC: 740 AN: 2112

Alfa AF: 0.408 Hom.: 56425

Bravo AF: 0.327

Asia WGS AF: 0.124 AC: 430 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	2.7
DANN	Benign	0.35
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs10245560; hg19: chr7-129199328;