rs1015465

Positions:

• chr6-30118563-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 0.17 in 152,208 control chromosomes in the GnomAD database, including 2,633 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 0.17 (2633 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25792 AN: 152090 Hom.: 2629 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.170 AC: 25824 AN: 152208 Hom.: 2633 Cov.: 33 AF XY: 0.167 AC XY: 12401 AN XY: 74438

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.201

Alfa AF: 0.140 Hom.: 2139

Bravo AF: 0.189

Asia WGS AF: 0.122 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015465; hg19: chr6-30086340;