chr15-95829400-G-A

Variant names:

• chr15-95829400-G-A
• rs744738

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 0.0859 in 152,208 control chromosomes in the GnomAD database, including 788 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 0.086 (788 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.81
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.271 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: 0.0859 AC: 13063 AN: 152088 Hom.: 784 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0614

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.0859 AC: 13074 AN: 152208 Hom.: 788 Cov.: 32 AF XY: 0.0929 AC XY: 6915 AN XY: 74428

African (AFR) AF: 0.0722 AC: 3001 AN: 41552

American (AMR) AF: 0.110 AC: 1690 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0782 AC: 271 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1462 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1145 AN: 4812

European-Finnish (FIN) AF: 0.103 AC: 1090 AN: 10602

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0614 AC: 4176 AN: 68004

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0731 Hom.: 1860

Bravo AF: 0.0841

Asia WGS AF: 0.278 AC: 968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.2
DANN	Benign	0.41
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs744738; hg19: chr15-96372629;