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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373709	XR_001739755.2	n.2308A>T		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105373710	XR_923509.3	n.70+6096T>A		intron_variant	Intron 1 of 3
LOC105373710	XR_923510.3	n.70+6096T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;