2-154482647-G-A

Variant names:

• chr2-154482647-G-A
• rs1366750
• XR_923485.4:n.115+6137C>T

Variant summary

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

The XR_923485.4(LOC105373694):​n.115+6137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,064 control chromosomes in the GnomAD database, including 2,031 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 0.15 (2031 hom., cov: 32)
• Consequence: LOC105373694 XR_923485.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

Genes affected

LOC105373694 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.152 AC: 23064 AN: 151946 Hom.: 2018 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.152 AC: 23090 AN: 152064 Hom.: 2031 Cov.: 32 AF XY: 0.154 AC XY: 11454 AN XY: 74314

African (AFR) AF: 0.0942 AC: 3909 AN: 41502

American (AMR) AF: 0.222 AC: 3396 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.408 AC: 2094 AN: 5136

South Asian (SAS) AF: 0.166 AC: 799 AN: 4822

European-Finnish (FIN) AF: 0.142 AC: 1495 AN: 10560

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10395 AN: 67988

Other (OTH) AF: 0.162 AC: 342 AN: 2114

Alfa AF: 0.148 Hom.: 255

Bravo AF: 0.157

Asia WGS AF: 0.225 AC: 778 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.20
DANN	Benign	0.58
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs1366750; hg19: chr2-155339159;