rs10515710

Variant names:

• chr5-155592305-T-C
• rs10515710

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;