2-126573377-T-G

Variant names:

• chr2-126573377-T-G
• rs1550404
• XR_001739693.1:n.211-36860A>C

Variant summary

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

The XR_001739693.1(LOC105373602):​n.211-36860A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0499 in 152,236 control chromosomes in the GnomAD database, including 246 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 0.050 (246 hom., cov: 32)
• Consequence: LOC105373602 XR_001739693.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 6 publications found

Genes affected

LOC105373602 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0745 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: 0.0500 AC: 7600 AN: 152118 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.0376

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0762

Gnomad OTH AF: 0.0541

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

GnomAD4 genome AF: 0.0499 AC: 7604 AN: 152236 Hom.: 246 Cov.: 32 AF XY: 0.0478 AC XY: 3558 AN XY: 74448

African (AFR) AF: 0.0213 AC: 883 AN: 41534

American (AMR) AF: 0.0396 AC: 605 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0519 AC: 180 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5176

South Asian (SAS) AF: 0.0353 AC: 170 AN: 4818

European-Finnish (FIN) AF: 0.0376 AC: 399 AN: 10620

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0762 AC: 5184 AN: 68010

Other (OTH) AF: 0.0536 AC: 113 AN: 2110

Alfa AF: 0.0670 Hom.: 1239

Bravo AF: 0.0480

Asia WGS AF: 0.0120 AC: 43 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.48
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1550404; hg19: chr2-127330954;