2-237235160-G-T

Position:

• chr2-237235160-G-T

Variant summary

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

The XR_924035.3(LOC105373953):​n.1437G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 151,934 control chromosomes in the GnomAD database, including 30,929 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 0.61 (30929 hom., cov: 30)
• Consequence: LOC105373953 XR_924035.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691

Genes affected

LOC105373953 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373953	XR_924035.3	n.1437G>T		non_coding_transcript_exon_variant	4/6
LOC105373953	XR_924034.3	n.321+8900G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93320 AN: 151814 Hom.: 30869 Cov.: 30

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.615 AC: 93438 AN: 151934 Hom.: 30929 Cov.: 30 AF XY: 0.609 AC XY: 45218 AN XY: 74230

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.618

Alfa AF: 0.523 Hom.: 40332

Bravo AF: 0.631

Asia WGS AF: 0.590 AC: 2056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4490127; hg19: chr2-238143803;