rs718035

chr15-95636515-C-Achr15-95636515-C-Gchr15-95636515-C-T

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 0.121 in 152,114 control chromosomes in the GnomAD database, including 2,537 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 0.12 (2537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.121 AC: 18389 AN: 151996 Hom.: 2528 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0649

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0847

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

GnomAD4 genome AF: 0.121 AC: 18428 AN: 152114 Hom.: 2537 Cov.: 32 AF XY: 0.125 AC XY: 9270 AN XY: 74360

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.0647

Gnomad4 ASJ AF: 0.0179

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0852

Alfa AF: 0.0199 Hom.: 54

Bravo AF: 0.130

Asia WGS AF: 0.268 AC: 932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.89
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs718035; hg19: chr15-96179744;