rs9582694

Positions:

• chr13-103373924-A-C

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-18303A>C 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 0.165 in 151,952 control chromosomes in the GnomAD database, including 2,272 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 0.16 (2272 hom., cov: 32)
• Consequence: ENST00000648788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000648788.1	n.56-18303A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.165 AC: 24988 AN: 151834 Hom.: 2269 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.0979

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0544

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.165 AC: 25017 AN: 151952 Hom.: 2272 Cov.: 32 AF XY: 0.161 AC XY: 11960 AN XY: 74244

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0977

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.140

Alfa AF: 0.156 Hom.: 3869

Bravo AF: 0.162

Asia WGS AF: 0.0940 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9582694; hg19: chr13-104026274;