chr9-11254070-T-C

Variant names:

• chr9-11254070-T-C
• rs1387292
• XR_001746618.1:n.1649A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746618.1(LOC105375974):​n.1649A>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_001746618.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 3 publications found

Genes affected

LOC105375974 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375974	XR_001746618.1	n.1649A>G		non_coding_transcript_exon_variant	Exon 6 of 6
LOC105375974	XR_007061893.1	n.1394A>G		non_coding_transcript_exon_variant	Exon 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230365	ENST00000799517.1	n.515+21335A>G		intron_variant	Intron 4 of 5
ENSG00000230365	ENST00000799518.1	n.398+21335A>G		intron_variant	Intron 3 of 4

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

African (AFR) AF: 0.382 AC: 15809 AN: 41398

American (AMR) AF: 0.579 AC: 8824 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3100 AN: 5122

South Asian (SAS) AF: 0.667 AC: 3211 AN: 4816

European-Finnish (FIN) AF: 0.502 AC: 5294 AN: 10548

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.486 AC: 33007 AN: 67906

Other (OTH) AF: 0.487 AC: 1028 AN: 2110

Alfa AF: 0.486 Hom.: 74830

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
PhyloP100		0.055

Splicing

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

Other links and lift over

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