rs7324557

Variant names:

• chr13-23722723-A-G
• rs7324557
• ENST00000691844.2:n.384+6106A>G

Your query was ambiguous. Multiple possible variants found:

• chr13-23722723-A-G
• chr13-23722723-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000691844.2(ENSG00000289332):​n.384+6106A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 151,268 control chromosomes in the GnomAD database, including 36,079 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 0.69 (36079 hom., cov: 29)
• Consequence: ENSG00000289332 ENST00000691844.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

ENSG00000289332 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.733 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
ENSG00000289332	ENST00000691844.2	n.384+6106A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.690 AC: 104282 AN: 151152 Hom.: 36045 Cov.: 29

Gnomad AFR AF: 0.740

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.684

Gnomad EAS AF: 0.694

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.690 AC: 104369 AN: 151268 Hom.: 36079 Cov.: 29 AF XY: 0.688 AC XY: 50805 AN XY: 73794

Gnomad4 AFR AF: 0.740

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.684

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.695

Alfa AF: 0.670 Hom.: 71327

Bravo AF: 0.693

Asia WGS AF: 0.696 AC: 2425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7324557; hg19: chr13-24296862;