rs952489

Positions:

• chr11-35010029-G-A
• chr11-35010029-G-T

Variant summary

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

The XR_001748180.2(LOC105376626):​n.8944C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 152,146 control chromosomes in the GnomAD database, including 28,811 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 0.59 (28811 hom., cov: 32)
• Consequence: LOC105376626 XR_001748180.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

Genes affected

LOC105376626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.8944C>T		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDHX	ENST00000477173.3	n.162-10179G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89827 AN: 152028 Hom.: 28825 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.590 AC: 89809 AN: 152146 Hom.: 28811 Cov.: 32 AF XY: 0.592 AC XY: 43997 AN XY: 74376

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.599

Alfa AF: 0.586 Hom.: 3355

Bravo AF: 0.572

Asia WGS AF: 0.656 AC: 2283 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952489; hg19: chr11-35031576;