rs17459015

Variant names:

• chr6-104369900-T-C
• rs17459015

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 0.138 in 152,196 control chromosomes in the GnomAD database, including 1,905 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 0.14 (1905 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 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: 0.139 AC: 21063 AN: 152078 Hom.: 1906 Cov.: 32

Gnomad AFR AF: 0.0331

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.138 AC: 21059 AN: 152196 Hom.: 1905 Cov.: 32 AF XY: 0.138 AC XY: 10285 AN XY: 74416

Gnomad4 AFR AF: 0.0330

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.175

Gnomad4 EAS AF: 0.109

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.212

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.111

Alfa AF: 0.178 Hom.: 3660

Bravo AF: 0.124

Asia WGS AF: 0.149 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17459015; hg19: chr6-104817775; COSMIC: COSV60261965;