15-44724147-A-G

Position:

• chr15-44724147-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.888

Gnomad4 AMR AF: 0.846

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.834

Gnomad4 SAS AF: 0.839

Gnomad4 FIN AF: 0.875

Gnomad4 NFE AF: 0.895

Gnomad4 OTH AF: 0.868

Alfa AF: 0.889 Hom.: 16292

Bravo AF: 0.880

Asia WGS AF: 0.810 AC: 2819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7165535; hg19: chr15-45016345;