2-53038991-C-T

Position:

• chr2-53038991-C-T

Variant summary

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

The XR_002959384.2(LOC105369165):​n.49-128967G>A 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 0.692 in 151,706 control chromosomes in the GnomAD database, including 37,895 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 0.69 (37895 hom., cov: 31)
• Consequence: LOC105369165 XR_002959384.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.465

Genes affected

LOC105369165 (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 (AFR) allele frequency at 95% confidence interval = 0.905 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369165	XR_002959384.2	n.49-128967G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 104893 AN: 151588 Hom.: 37836 Cov.: 31

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.692 AC: 105011 AN: 151706 Hom.: 37895 Cov.: 31 AF XY: 0.692 AC XY: 51292 AN XY: 74112

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.645

Alfa AF: 0.600 Hom.: 41094

Bravo AF: 0.687

Asia WGS AF: 0.702 AC: 2432 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.28
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2357013; hg19: chr2-53266129;