rs7324557

chr13-23722723-A-Gchr13-23722723-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, non coding transcript 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: ENST00000691844.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.372

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691844.2	n.384+6106A>G		intron_variant, non_coding_transcript_variant

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;