chr9-2681175-T-A

Variant names:

• chr9-2681175-T-A
• rs10967492
• XR_929436.3:n.13287A>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC105375957 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000768783.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286670	ENST00000768783.1		n.114-13114A>T		intron	N/A
	ENSG00000286670	ENST00000768784.1		n.157-13114A>T		intron	N/A
	ENSG00000286670	ENST00000768785.1		n.157-16100A>T		intron	N/A

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

African (AFR) AF: 0.116 AC: 4806 AN: 41452

American (AMR) AF: 0.180 AC: 2750 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1020 AN: 3468

East Asian (EAS) AF: 0.273 AC: 1407 AN: 5154

South Asian (SAS) AF: 0.295 AC: 1419 AN: 4816

European-Finnish (FIN) AF: 0.200 AC: 2116 AN: 10582

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13699 AN: 68006

Other (OTH) AF: 0.181 AC: 381 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.6
DANN	Benign	0.42
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10967492; hg19: chr9-2681175;