rs1550404

chr2-126573377-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001739693.1(LOC105373602):n.211-36860A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

LOC105373602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105373602	XR_001739693.1	n.211-36860A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0213

Gnomad4 AMR AF: 0.0396

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0353

Gnomad4 FIN AF: 0.0376

Gnomad4 NFE AF: 0.0762

Gnomad4 OTH AF: 0.0536

Alfa AF: 0.0705 Hom.: 882

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1550404; hg19: chr2-127330954;