rs2027432

chr1-247415139-A-Gchr1-247415139-A-T

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 0.833 in 152,176 control chromosomes in the GnomAD database, including 52,878 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 0.83 (52878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.904 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: 0.833 AC: 126641 AN: 152058 Hom.: 52830 Cov.: 31

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.855

Gnomad ASJ AF: 0.827

Gnomad EAS AF: 0.925

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.833 AC: 126749 AN: 152176 Hom.: 52878 Cov.: 31 AF XY: 0.833 AC XY: 62001 AN XY: 74408

Gnomad4 AFR AF: 0.838

Gnomad4 AMR AF: 0.856

Gnomad4 ASJ AF: 0.827

Gnomad4 EAS AF: 0.925

Gnomad4 SAS AF: 0.754

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.824

Alfa AF: 0.815 Hom.: 65850

Bravo AF: 0.837

Asia WGS AF: 0.853 AC: 2967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.66
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2027432; hg19: chr1-247578441;