15-44724147-A-G

Variant names:

• chr15-44724147-A-G
• rs7165535

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 0.883 in 152,142 control chromosomes in the GnomAD database, including 59,420 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 0.88 (59420 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 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: 0.883 AC: 134243 AN: 152024 Hom.: 59378 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.847

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.834

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.883 AC: 134342 AN: 152142 Hom.: 59420 Cov.: 31 AF XY: 0.882 AC XY: 65624 AN XY: 74380

African (AFR) AF: 0.888 AC: 36849 AN: 41502

American (AMR) AF: 0.846 AC: 12921 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.890 AC: 3088 AN: 3468

East Asian (EAS) AF: 0.834 AC: 4331 AN: 5192

South Asian (SAS) AF: 0.839 AC: 4046 AN: 4824

European-Finnish (FIN) AF: 0.875 AC: 9240 AN: 10564

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60886 AN: 68004

Other (OTH) AF: 0.868 AC: 1834 AN: 2112

Alfa AF: 0.888 Hom.: 19638

Bravo AF: 0.880

Asia WGS AF: 0.810 AC: 2819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.6
DANN	Benign	0.72
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs7165535; hg19: chr15-45016345;