rs9288534

Positions:

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

Variant summary

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

The XR_007088689.1(LOC105373703):​n.635-26626C>T variant causes a intron, non coding transcript 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_007088689.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

Genes affected

LOC105373703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373703	XR_007088689.1	n.635-26626C>T		intron_variant, non_coding_transcript_variant
LOC105373703	XR_001739749.2	n.852C>T		non_coding_transcript_exon_variant	5/8
LOC105373703	XR_001739750.2	n.852C>T		non_coding_transcript_exon_variant	5/6
LOC105373703	XR_001739751.2	n.852C>T		non_coding_transcript_exon_variant	5/7

Ensembl

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

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

Gnomad4 AFR AF: 0.510

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.360

Alfa AF: 0.285 Hom.: 6559

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288534; hg19: chr2-156697282;