rs9288534

Variant names:

• chr2-155840770-G-A
• rs9288534
• XR_001739749.2:n.852C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-155840770-G-A
• chr2-155840770-G-C
• chr2-155840770-G-T

Variant summary

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

The XR_001739749.2(LOC105373703):​n.852C>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 0.364 in 151,874 control chromosomes in the GnomAD database, including 11,085 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 0.36 (11085 hom., cov: 32)
• Consequence: LOC105373703 XR_001739749.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750
• Publications: 4 publications found

Genes affected

LOC105373703 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373703	XR_001739749.2	n.852C>T		non_coding_transcript_exon_variant	Exon 5 of 8
LOC105373703	XR_001739750.2	n.852C>T		non_coding_transcript_exon_variant	Exon 5 of 6
LOC105373703	XR_001739751.2	n.852C>T		non_coding_transcript_exon_variant	Exon 5 of 7
LOC105373703	XR_007088689.1	n.635-26626C>T		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304068	ENST00000799383.1	n.877-30762C>T		intron_variant	Intron 6 of 8
ENSG00000304068	ENST00000799384.1	n.694-26626C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55170 AN: 151756 Hom.: 11058 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.364 AC: 55246 AN: 151874 Hom.: 11085 Cov.: 32 AF XY: 0.371 AC XY: 27547 AN XY: 74226

African (AFR) AF: 0.510 AC: 21141 AN: 41446

American (AMR) AF: 0.331 AC: 5045 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1054 AN: 3462

East Asian (EAS) AF: 0.568 AC: 2926 AN: 5150

South Asian (SAS) AF: 0.478 AC: 2305 AN: 4826

European-Finnish (FIN) AF: 0.332 AC: 3504 AN: 10552

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18243 AN: 67874

Other (OTH) AF: 0.360 AC: 760 AN: 2110

Alfa AF: 0.307 Hom.: 13326

Bravo AF: 0.367

Asia WGS AF: 0.492 AC: 1713 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.29
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs9288534; hg19: chr2-156697282;