rs10515621

Variant names:

• chr5-148866981-T-C
• rs10515621

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 0.106 in 152,220 control chromosomes in the GnomAD database, including 1,135 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 0.11 (1135 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 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: 0.106 AC: 16086 AN: 152102 Hom.: 1134 Cov.: 32

Gnomad AFR AF: 0.0274

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0994

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0371

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.106 AC: 16082 AN: 152220 Hom.: 1135 Cov.: 32 AF XY: 0.103 AC XY: 7648 AN XY: 74414

Gnomad4 AFR AF: 0.0274

Gnomad4 AMR AF: 0.0992

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0369

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.118

Alfa AF: 0.140 Hom.: 773

Bravo AF: 0.102

Asia WGS AF: 0.0200 AC: 72 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.44
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515621; hg19: chr5-148246544;