chr9-11254070-T-C

Position:

• chr9-11254070-T-C

Variant summary

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

The XR_007061893.1(LOC105375974):​n.1394A>G 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 0.48 in 151,812 control chromosomes in the GnomAD database, including 18,014 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 0.48 (18014 hom., cov: 32)
• Consequence: LOC105375974 XR_007061893.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

LOC105375974 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.648 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375974	XR_007061893.1	n.1394A>G		non_coding_transcript_exon_variant	5/5
LOC105375974	XR_001746618.1	n.1649A>G		non_coding_transcript_exon_variant	6/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72816 AN: 151696 Hom.: 18002 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.480 AC: 72852 AN: 151812 Hom.: 18014 Cov.: 32 AF XY: 0.489 AC XY: 36261 AN XY: 74182

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.487

Alfa AF: 0.491 Hom.: 37550

Bravo AF: 0.477

Asia WGS AF: 0.663 AC: 2302 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1387292; hg19: chr9-11254070; COSMIC: COSV69446797;