15-38441646-A-G

Variant names:

• chr15-38441646-A-G
• rs8029989

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 0.644 in 152,010 control chromosomes in the GnomAD database, including 31,850 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 0.64 (31850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.332

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97767 AN: 151892 Hom.: 31805 Cov.: 32

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.690

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.644 AC: 97869 AN: 152010 Hom.: 31850 Cov.: 32 AF XY: 0.649 AC XY: 48188 AN XY: 74280

Gnomad4 AFR AF: 0.654

Gnomad4 AMR AF: 0.690

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.635

Alfa AF: 0.623 Hom.: 3977

Bravo AF: 0.643

Asia WGS AF: 0.813 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	4.0
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8029989; hg19: chr15-38733847;