rs7543509

Variant names:

• chr1-110509377-A-G
• rs7543509

Your query was ambiguous. Multiple possible variants found:

• chr1-110509377-A-G
• chr1-110509377-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 0.0852 in 152,190 control chromosomes in the GnomAD database, including 691 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 0.085 (691 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

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 = 0.211 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: 0.0853 AC: 12976 AN: 152072 Hom.: 691 Cov.: 33

Gnomad AFR AF: 0.0730

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.132

Gnomad ASJ AF: 0.0370

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0749

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.0727

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

GnomAD4 genome AF: 0.0852 AC: 12973 AN: 152190 Hom.: 691 Cov.: 33 AF XY: 0.0876 AC XY: 6516 AN XY: 74416

Gnomad4 AFR AF: 0.0729

Gnomad4 AMR AF: 0.132

Gnomad4 ASJ AF: 0.0370

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.0749

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.0705

Alfa AF: 0.0765 Hom.: 695

Bravo AF: 0.0902

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7543509; hg19: chr1-111051999;