15-26178900-C-G

Variant names:

• chr15-26178900-C-G
• rs547843

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 0.322 in 151,810 control chromosomes in the GnomAD database, including 8,222 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 0.32 (8222 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 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: 0.321 AC: 48754 AN: 151692 Hom.: 8202 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.347

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.322 AC: 48817 AN: 151810 Hom.: 8222 Cov.: 31 AF XY: 0.330 AC XY: 24483 AN XY: 74184

African (AFR) AF: 0.353 AC: 14603 AN: 41408

American (AMR) AF: 0.305 AC: 4651 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 840 AN: 3464

East Asian (EAS) AF: 0.570 AC: 2911 AN: 5110

South Asian (SAS) AF: 0.510 AC: 2452 AN: 4804

European-Finnish (FIN) AF: 0.384 AC: 4039 AN: 10530

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18381 AN: 67920

Other (OTH) AF: 0.322 AC: 679 AN: 2110

Alfa AF: 0.116 Hom.: 155

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.11
DANN	Benign	0.43
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs547843; hg19: chr15-26424047;