rs9587583

Positions:

• chr13-108437268-G-A
• chr13-108437268-G-T

Variant summary

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

The ENST00000636252.1(ENSG00000283384):​n.334-9914G>A 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 0.0883 in 152,146 control chromosomes in the GnomAD database, including 613 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 0.088 (613 hom., cov: 32)
• Consequence: ENST00000636252.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 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
	ENST00000636252.1	n.334-9914G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0884 AC: 13432 AN: 152028 Hom.: 613 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0616

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0883

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0834

Gnomad OTH AF: 0.0920

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

GnomAD4 genome AF: 0.0883 AC: 13435 AN: 152146 Hom.: 613 Cov.: 32 AF XY: 0.0862 AC XY: 6412 AN XY: 74378

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.0613

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.0927

Gnomad4 SAS AF: 0.0637

Gnomad4 FIN AF: 0.0883

Gnomad4 NFE AF: 0.0834

Gnomad4 OTH AF: 0.0920

Alfa AF: 0.0795 Hom.: 632

Bravo AF: 0.0878

Asia WGS AF: 0.112 AC: 389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.94
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9587583; hg19: chr13-109089616;