rs7543390

Variant names:

• chr1-79752889-A-C
• rs7543390

Your query was ambiguous. Multiple possible variants found:

• chr1-79752889-A-C
• chr1-79752889-A-G
• chr1-79752889-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.805 AC: 33336 AN: 41418

American (AMR) AF: 0.947 AC: 14476 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.959 AC: 4968 AN: 5178

South Asian (SAS) AF: 0.886 AC: 4273 AN: 4824

European-Finnish (FIN) AF: 0.973 AC: 10313 AN: 10598

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.964 AC: 65510 AN: 67976

Other (OTH) AF: 0.916 AC: 1927 AN: 2104

Alfa AF: 0.935 Hom.: 10594

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
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7543390; hg19: chr1-80218574;