rs2111485

chr2-162254026-A-G

Variant summary

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

The XR_923544.3(LOC105373724):n.681+3739A>G 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 0.461 in 151,990 control chromosomes in the GnomAD database, including 18,447 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 0.46 (18447 hom., cov: 31)
• Consequence: LOC105373724 XR_923544.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430

Genes affected

LOC105373724 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373724	XR_923544.3	n.681+3739A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.461 AC: 70088 AN: 151872 Hom.: 18450 Cov.: 31

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.461 AC: 70082 AN: 151990 Hom.: 18447 Cov.: 31 AF XY: 0.455 AC XY: 33825 AN XY: 74300

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.443

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.474

Alfa AF: 0.574 Hom.: 51701

Bravo AF: 0.438

Asia WGS AF: 0.283 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.5
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2111485; hg19: chr2-163110536;