rs9536919

chr13-54949643-A-Gchr13-54949643-A-T

Variant summary

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

The ENST00000667279.1(ENSG00000277047):n.629+7588A>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 0.703 in 152,090 control chromosomes in the GnomAD database, including 38,814 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 0.70 (38814 hom., cov: 33)
• Consequence: ENST00000667279.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903233	XR_007063916.1	n.272+7588A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000667279.1	n.629+7588A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106882 AN: 151972 Hom.: 38806 Cov.: 33

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.675

Gnomad AMR AF: 0.753

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.642

Gnomad SAS AF: 0.695

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.703 AC: 106923 AN: 152090 Hom.: 38814 Cov.: 33 AF XY: 0.701 AC XY: 52109 AN XY: 74352

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.802

Gnomad4 OTH AF: 0.720

Alfa AF: 0.770 Hom.: 20463

Bravo AF: 0.695

Asia WGS AF: 0.612 AC: 2129 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	7.1
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9536919; hg19: chr13-55523778;