rs11689287

Positions:

• chr2-127130761-T-C

Variant summary

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

The XR_923311.4(LOC105373605):​n.846-2477T>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 0.129 in 150,540 control chromosomes in the GnomAD database, including 1,355 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 0.13 (1355 hom., cov: 30)
• Consequence: LOC105373605 XR_923311.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

Genes affected

LOC105373605 (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 (NFE) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373605	XR_923311.4	n.846-2477T>C		intron_variant, non_coding_transcript_variant
LOC105373605	XR_923310.3	n.449-2477T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19360 AN: 150434 Hom.: 1352 Cov.: 30

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0586

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.129 AC: 19375 AN: 150540 Hom.: 1355 Cov.: 30 AF XY: 0.125 AC XY: 9225 AN XY: 73518

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.100

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.124

Alfa AF: 0.150 Hom.: 176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.052
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11689287; hg19: chr2-127888337; COSMIC: COSV65787146;