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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373602	XR_001739693.1	n.211-36860A>C		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;