rs10495669

chr2-17844006-C-G

Variant summary

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

The XR_939764.2(LOC112267888):n.447+3688G>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 0.505 in 152,138 control chromosomes in the GnomAD database, including 20,270 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 0.50 (20270 hom., cov: 33)
• Consequence: LOC112267888 XR_939764.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10

Genes affected

LOC112267888 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267888	XR_939764.2	n.447+3688G>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76762 AN: 152020 Hom.: 20256 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.0505

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.533

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.505 AC: 76816 AN: 152138 Hom.: 20270 Cov.: 33 AF XY: 0.499 AC XY: 37106 AN XY: 74376

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.0503

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.533

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.528

Alfa AF: 0.530 Hom.: 2721

Bravo AF: 0.494

Asia WGS AF: 0.250 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.0030
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10495669; hg19: chr2-18025273;