rs12555508

Positions:

• chr9-85406281-G-A

Variant summary

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

The ENST00000669133.1(ENSG00000285634):​n.142-3594C>T 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 0.105 in 152,232 control chromosomes in the GnomAD database, including 1,173 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 0.11 (1173 hom., cov: 33)
• Consequence: ENST00000669133.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.525

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 (AMR) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376121	XR_001746810.2	n.312-3594C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000669133.1	n.142-3594C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15970 AN: 152114 Hom.: 1159 Cov.: 33

Gnomad AFR AF: 0.0259

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0534

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.105 AC: 15990 AN: 152232 Hom.: 1173 Cov.: 33 AF XY: 0.109 AC XY: 8078 AN XY: 74434

Gnomad4 AFR AF: 0.0258

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.144

Gnomad4 EAS AF: 0.0532

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.105

Alfa AF: 0.122 Hom.: 230

Bravo AF: 0.108

Asia WGS AF: 0.0800 AC: 277 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	0.33
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12555508; hg19: chr9-88021196;