rs10515710

chr5-155592305-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0424 in 152,324 control chromosomes in the GnomAD database, including 170 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 0.042 (170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

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: 0.0425 AC: 6466 AN: 152206 Hom.: 170 Cov.: 33

Gnomad AFR AF: 0.0218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0857

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0424 AC: 6458 AN: 152324 Hom.: 170 Cov.: 33 AF XY: 0.0429 AC XY: 3196 AN XY: 74492

Gnomad4 AFR AF: 0.0217

Gnomad4 AMR AF: 0.0297

Gnomad4 ASJ AF: 0.0901

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0855

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0564

Gnomad4 OTH AF: 0.0431

Alfa AF: 0.0550 Hom.: 126

Bravo AF: 0.0383

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.9
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515710; hg19: chr5-154971865; COSMIC: COSV60218930;