chr1-47515324-A-G

Position:

• chr1-47515324-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 0.902 in 152,194 control chromosomes in the GnomAD database, including 62,297 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 0.90 (62297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137126 AN: 152076 Hom.: 62249 Cov.: 31

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.967

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.938

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.898

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.906

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

GnomAD4 genome AF: 0.902 AC: 137229 AN: 152194 Hom.: 62297 Cov.: 31 AF XY: 0.901 AC XY: 67075 AN XY: 74408

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.938

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.898

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.898

Gnomad4 OTH AF: 0.906

Alfa AF: 0.904 Hom.: 12628

Bravo AF: 0.890

Asia WGS AF: 0.792 AC: 2755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs513464; hg19: chr1-47980996;