15-74734838-A-G

Variant names:

• chr15-74734838-A-G
• rs17861120

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 0.153 in 152,160 control chromosomes in the GnomAD database, including 2,755 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 0.15 (2755 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23219 AN: 152042 Hom.: 2734 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.153 AC: 23286 AN: 152160 Hom.: 2755 Cov.: 32 AF XY: 0.162 AC XY: 12042 AN XY: 74400

African (AFR) AF: 0.157 AC: 6496 AN: 41508

American (AMR) AF: 0.316 AC: 4827 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.502 AC: 2600 AN: 5176

South Asian (SAS) AF: 0.343 AC: 1654 AN: 4824

European-Finnish (FIN) AF: 0.112 AC: 1189 AN: 10596

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.0819 AC: 5572 AN: 67996

Other (OTH) AF: 0.165 AC: 349 AN: 2112

Alfa AF: 0.118 Hom.: 217

Bravo AF: 0.166

Asia WGS AF: 0.452 AC: 1565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.4
DANN	Benign	0.71
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17861120; hg19: chr15-75027179;