15-63041420-A-G

Position:

• chr15-63041420-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.696 in 152,206 control chromosomes in the GnomAD database, including 37,029 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 0.70 (37029 hom., cov: 34)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.63041420A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105867 AN: 152088 Hom.: 36990 Cov.: 34

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.696 AC: 105954 AN: 152206 Hom.: 37029 Cov.: 34 AF XY: 0.692 AC XY: 51480 AN XY: 74394

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.544

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.694

Alfa AF: 0.699 Hom.: 5515

Bravo AF: 0.705

Asia WGS AF: 0.552 AC: 1919 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	17
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3809565; hg19: chr15-63333619;