rs10967492

chr9-2681175-T-A

Variant summary

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

The XR_929436.3(LOC105375957):n.13287A>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 0.183 in 152,068 control chromosomes in the GnomAD database, including 2,754 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 0.18 (2754 hom., cov: 32)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.26

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375957	XR_929436.3	n.13287A>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27868 AN: 151948 Hom.: 2755 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.183 AC: 27878 AN: 152068 Hom.: 2754 Cov.: 32 AF XY: 0.188 AC XY: 13947 AN XY: 74316

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.294

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.200

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.181

Alfa AF: 0.182 Hom.: 339

Bravo AF: 0.177

Asia WGS AF: 0.253 AC: 878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.6
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10967492; hg19: chr9-2681175;