15-25649511-C-T

Variant names:

• chr15-25649511-C-T
• rs6576443

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 0.408 in 152,094 control chromosomes in the GnomAD database, including 14,017 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 0.41 (14017 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 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: 0.408 AC: 62042 AN: 151976 Hom.: 13992 Cov.: 33

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.408 AC: 62124 AN: 152094 Hom.: 14017 Cov.: 33 AF XY: 0.404 AC XY: 30074 AN XY: 74358

African (AFR) AF: 0.615 AC: 25465 AN: 41436

American (AMR) AF: 0.312 AC: 4777 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1224 AN: 3468

East Asian (EAS) AF: 0.149 AC: 774 AN: 5180

South Asian (SAS) AF: 0.306 AC: 1478 AN: 4824

European-Finnish (FIN) AF: 0.329 AC: 3479 AN: 10576

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23641 AN: 68004

Other (OTH) AF: 0.392 AC: 827 AN: 2110

Alfa AF: 0.367 Hom.: 45518

Bravo AF: 0.418

Asia WGS AF: 0.271 AC: 945 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		0.098

Splicing

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

Other links and lift over

dbSNP: rs6576443; hg19: chr15-25894658;