rs7543509

Variant names:

• chr1-110509377-A-G
• rs7543509
• ENST00000779684.1:n.86+1097A>G

Your query was ambiguous. Multiple possible variants found:

• chr1-110509377-A-G
• chr1-110509377-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000779684.1(ENSG00000301555):​n.86+1097A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000301555 ENST00000779684.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 2 publications found

Genes affected

ENSG00000301555 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000301555	ENST00000779684.1	n.86+1097A>G		intron_variant	Intron 1 of 1
ENSG00000301572	ENST00000779905.1	n.183+567T>C		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.0729 AC: 3027 AN: 41524

American (AMR) AF: 0.132 AC: 2012 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0370 AC: 128 AN: 3462

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5174

South Asian (SAS) AF: 0.124 AC: 597 AN: 4824

European-Finnish (FIN) AF: 0.0749 AC: 794 AN: 10600

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0740 AC: 5032 AN: 67992

Other (OTH) AF: 0.0705 AC: 149 AN: 2112

Alfa AF: 0.0775 Hom.: 1038

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
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7543509; hg19: chr1-111051999;