chr15-62135165-C-T

Variant names:

• chr15-62135165-C-T
• rs6494311

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 0.378 in 152,128 control chromosomes in the GnomAD database, including 11,064 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 0.38 (11064 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107

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 (AMR) allele frequency at 95% confidence interval = 0.416 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: 0.378 AC: 57485 AN: 152010 Hom.: 11046 Cov.: 33

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.378 AC: 57535 AN: 152128 Hom.: 11064 Cov.: 33 AF XY: 0.377 AC XY: 28034 AN XY: 74360

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.350

Gnomad4 FIN AF: 0.381

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.408

Alfa AF: 0.411 Hom.: 26826

Bravo AF: 0.376

Asia WGS AF: 0.321 AC: 1118 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6494311; hg19: chr15-62427364;