rs9582695

Positions:

• chr13-103384086-A-G
• chr13-103384086-A-T

Variant summary

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

The ENST00000648788.1(ENSG00000285789):​n.56-8141A>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 0.134 in 152,100 control chromosomes in the GnomAD database, including 1,502 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 0.13 (1502 hom., cov: 32)
• Consequence: ENST00000648788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.164 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
	ENST00000648788.1	n.56-8141A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20448 AN: 151982 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.134 AC: 20450 AN: 152100 Hom.: 1502 Cov.: 32 AF XY: 0.131 AC XY: 9722 AN XY: 74370

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0912

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.117

Alfa AF: 0.141 Hom.: 788

Bravo AF: 0.128

Asia WGS AF: 0.0660 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	0.36
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9582695; hg19: chr13-104036436;