2-157050092-A-T

Variant names:

• chr2-157050092-A-T
• rs1481384
• XR_001739755.2:n.2308A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739755.2(LOC105373709):​n.2308A>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 0.603 in 151,906 control chromosomes in the GnomAD database, including 28,328 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 0.60 (28328 hom., cov: 31)
• Consequence: LOC105373709 XR_001739755.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 5 publications found

Genes affected

LOC105373709 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91520 AN: 151788 Hom.: 28306 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.603 AC: 91582 AN: 151906 Hom.: 28328 Cov.: 31 AF XY: 0.604 AC XY: 44801 AN XY: 74216

African (AFR) AF: 0.471 AC: 19516 AN: 41406

American (AMR) AF: 0.708 AC: 10797 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3470

East Asian (EAS) AF: 0.431 AC: 2224 AN: 5160

South Asian (SAS) AF: 0.658 AC: 3170 AN: 4814

European-Finnish (FIN) AF: 0.644 AC: 6799 AN: 10552

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45067 AN: 67930

Other (OTH) AF: 0.600 AC: 1269 AN: 2114

Alfa AF: 0.516 Hom.: 1537

Bravo AF: 0.599

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.68
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs1481384; hg19: chr2-157906604;