rs837841

chr2-129276439-C-Achr2-129276439-C-Gchr2-129276439-C-T

Variant summary

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

The XR_007087234.1(LOC105373612):n.277-12511C>A 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 0.432 in 151,968 control chromosomes in the GnomAD database, including 14,644 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 0.43 (14644 hom., cov: 33)
• Consequence: LOC105373612 XR_007087234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181

Genes affected

LOC105373612 (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 (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373612	XR_007087234.1	n.277-12511C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65521 AN: 151852 Hom.: 14622 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.450

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.432 AC: 65586 AN: 151968 Hom.: 14644 Cov.: 33 AF XY: 0.435 AC XY: 32305 AN XY: 74286

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.405

Alfa AF: 0.385 Hom.: 11951

Bravo AF: 0.449

Asia WGS AF: 0.583 AC: 2029 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	0.19
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs837841; hg19: chr2-130034012;