15-74708889-C-G

Variant names:

• chr15-74708889-C-G
• rs2198843

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 0.307 in 151,942 control chromosomes in the GnomAD database, including 9,705 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 0.31 (9705 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 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: 0.306 AC: 46531 AN: 151824 Hom.: 9659 Cov.: 31

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.307 AC: 46651 AN: 151942 Hom.: 9705 Cov.: 31 AF XY: 0.311 AC XY: 23100 AN XY: 74276

African (AFR) AF: 0.545 AC: 22549 AN: 41374

American (AMR) AF: 0.415 AC: 6335 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2702 AN: 5162

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4808

European-Finnish (FIN) AF: 0.144 AC: 1528 AN: 10584

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

European-Non Finnish (NFE) AF: 0.148 AC: 10058 AN: 67976

Other (OTH) AF: 0.302 AC: 638 AN: 2110

Alfa AF: 0.0727 Hom.: 91

Bravo AF: 0.336

Asia WGS AF: 0.500 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.0
DANN	Benign	0.65
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs2198843; hg19: chr15-75001230;