rs10499725

chr7-53985565-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0155 in 152,318 control chromosomes in the GnomAD database, including 27 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 0.015 (27 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0155 (2356/152318) while in subpopulation NFE AF= 0.018 (1223/68018). AF 95% confidence interval is 0.0171. There are 27 homozygotes in gnomad4. There are 1119 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 27 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2358 AN: 152202 Hom.: 27 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0177

Gnomad ASJ AF: 0.0421

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00791

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0180

Gnomad OTH AF: 0.0248

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

GnomAD4 genome AF: 0.0155 AC: 2356 AN: 152318 Hom.: 27 Cov.: 32 AF XY: 0.0150 AC XY: 1119 AN XY: 74484

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0176

Gnomad4 ASJ AF: 0.0421

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00435

Gnomad4 FIN AF: 0.00791

Gnomad4 NFE AF: 0.0180

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0144 Hom.: 2

Bravo AF: 0.0170

Asia WGS AF: 0.00318 AC: 11 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.6
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10499725; hg19: chr7-54053258;