chr15-74746626-G-A

Variant names:

• chr15-74746626-G-A
• rs2069521

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 0.0486 in 152,278 control chromosomes in the GnomAD database, including 267 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 0.049 (267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7397 AN: 152160 Hom.: 267 Cov.: 32

Gnomad AFR AF: 0.0936

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0334

Gnomad ASJ AF: 0.0576

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0375

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0218

Gnomad OTH AF: 0.0425

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

GnomAD4 genome AF: 0.0486 AC: 7395 AN: 152278 Hom.: 267 Cov.: 32 AF XY: 0.0498 AC XY: 3707 AN XY: 74454

African (AFR) AF: 0.0934 AC: 3879 AN: 41532

American (AMR) AF: 0.0333 AC: 509 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0576 AC: 200 AN: 3470

East Asian (EAS) AF: 0.0735 AC: 382 AN: 5194

South Asian (SAS) AF: 0.0857 AC: 414 AN: 4828

European-Finnish (FIN) AF: 0.0375 AC: 398 AN: 10612

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0218 AC: 1484 AN: 68036

Other (OTH) AF: 0.0421 AC: 89 AN: 2116

Alfa AF: 0.0390 Hom.: 49

Bravo AF: 0.0487

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.95
DANN	Benign	0.59
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2069521; hg19: chr15-75038967;