rs9288111

Positions:

• chr2-185199269-G-C

Variant summary

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

The XR_923661.1(LOC105373781):​n.363+2504G>C 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 0.325 in 151,042 control chromosomes in the GnomAD database, including 8,304 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 (8304 hom., cov: 32)
• Consequence: LOC105373781 XR_923661.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

Genes affected

LOC105373781 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373781	XR_923661.1	n.363+2504G>C		intron_variant, non_coding_transcript_variant
LOC105373781	XR_923662.1	n.333+2504G>C		intron_variant, non_coding_transcript_variant
LOC105373781	XR_923663.1	n.215-20385G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 48998 AN: 150926 Hom.: 8282 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.325 AC: 49055 AN: 151042 Hom.: 8304 Cov.: 32 AF XY: 0.326 AC XY: 24031 AN XY: 73768

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.318

Alfa AF: 0.336 Hom.: 1093

Bravo AF: 0.311

Asia WGS AF: 0.453 AC: 1552 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.015
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9288111; hg19: chr2-186063996;