15-60317231-C-T

Variant names:

• chr15-60317231-C-T
• rs11853426

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 0.442 in 151,758 control chromosomes in the GnomAD database, including 14,962 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 0.44 (14962 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.554 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: 0.442 AC: 67096 AN: 151640 Hom.: 14948 Cov.: 30

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.443

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.442 AC: 67145 AN: 151758 Hom.: 14962 Cov.: 30 AF XY: 0.444 AC XY: 32930 AN XY: 74118

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.443

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.441

Alfa AF: 0.423 Hom.: 1226

Bravo AF: 0.454

Asia WGS AF: 0.448 AC: 1559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11853426; hg19: chr15-60609430;