9-2691951-C-T

Variant names:

• chr9-2691951-C-T
• rs10122587
• XR_929436.3:n.2511G>A

Variant summary

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

The XR_929436.3(LOC105375957):​n.2511G>A 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 0.317 in 152,012 control chromosomes in the GnomAD database, including 8,042 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 0.32 (8042 hom., cov: 32)
• Consequence: LOC105375957 XR_929436.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 5 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375957	XR_929436.3	n.2511G>A		non_coding_transcript_exon_variant	Exon 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286670	ENST00000768783.1	n.114-23890G>A		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768784.1	n.157-23890G>A		intron_variant	Intron 1 of 3
ENSG00000286670	ENST00000768785.1	n.157-26876G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48124 AN: 151894 Hom.: 8025 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.257

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.317 AC: 48187 AN: 152012 Hom.: 8042 Cov.: 32 AF XY: 0.319 AC XY: 23694 AN XY: 74292

African (AFR) AF: 0.407 AC: 16856 AN: 41422

American (AMR) AF: 0.286 AC: 4363 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1421 AN: 3468

East Asian (EAS) AF: 0.402 AC: 2081 AN: 5174

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4810

European-Finnish (FIN) AF: 0.257 AC: 2713 AN: 10564

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18073 AN: 67976

Other (OTH) AF: 0.297 AC: 627 AN: 2114

Alfa AF: 0.277 Hom.: 10341

Bravo AF: 0.323

Asia WGS AF: 0.367 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.093
DANN	Benign	0.65
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs10122587; hg19: chr9-2691951; COSMIC: COSV60322055;