rs7543390

chr1-79752889-A-Cchr1-79752889-A-Gchr1-79752889-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 0.916 in 152,062 control chromosomes in the GnomAD database, including 64,112 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 0.92 (64112 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899

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 = 0.958 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: 0.916 AC: 139119 AN: 151946 Hom.: 64066 Cov.: 31

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.947

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.964

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.916 AC: 139221 AN: 152062 Hom.: 64112 Cov.: 31 AF XY: 0.915 AC XY: 68056 AN XY: 74340

Gnomad4 AFR AF: 0.805

Gnomad4 AMR AF: 0.947

Gnomad4 ASJ AF: 0.961

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.886

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.964

Gnomad4 OTH AF: 0.916

Alfa AF: 0.940 Hom.: 10349

Bravo AF: 0.910

Asia WGS AF: 0.903 AC: 3127 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	5.9
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543390; hg19: chr1-80218574;