chr15-62112183-C-T

Variant names:

• chr15-62112183-C-T
• rs1436955

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.299 in 152,070 control chromosomes in the GnomAD database, including 6,898 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 0.30 (6898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 43 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.36 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: 0.299 AC: 45448 AN: 151952 Hom.: 6865 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.299 AC: 45532 AN: 152070 Hom.: 6898 Cov.: 32 AF XY: 0.299 AC XY: 22256 AN XY: 74328

African (AFR) AF: 0.346 AC: 14327 AN: 41464

American (AMR) AF: 0.368 AC: 5625 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 912 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1193 AN: 5174

South Asian (SAS) AF: 0.244 AC: 1177 AN: 4816

European-Finnish (FIN) AF: 0.283 AC: 2991 AN: 10564

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18146 AN: 67978

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.279 Hom.: 27315

Bravo AF: 0.308

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.2
DANN	Benign	0.96
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1436955; hg19: chr15-62404382;