15-82123016-T-C

Variant names:

• chr15-82123016-T-C
• rs2665109

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 0.844 in 152,144 control chromosomes in the GnomAD database, including 54,871 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 0.84 (54871 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.844 AC: 128335 AN: 152026 Hom.: 54810 Cov.: 31

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.829

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.962

Gnomad FIN AF: 0.841

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.768

Gnomad OTH AF: 0.809

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

GnomAD4 genome AF: 0.844 AC: 128458 AN: 152144 Hom.: 54871 Cov.: 31 AF XY: 0.850 AC XY: 63257 AN XY: 74380

Gnomad4 AFR AF: 0.958

Gnomad4 AMR AF: 0.829

Gnomad4 ASJ AF: 0.766

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.962

Gnomad4 FIN AF: 0.841

Gnomad4 NFE AF: 0.768

Gnomad4 OTH AF: 0.810

Alfa AF: 0.782 Hom.: 64831

Bravo AF: 0.844

Asia WGS AF: 0.968 AC: 3364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2665109; hg19: chr15-82415357;