rs2376803

Variant names:

• chr1-2036515-C-T
• rs2376803
• XR_001737845.3:n.696G>A

Variant summary

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

The XR_001737845.3(LOC105378590):​n.696G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 152,208 control chromosomes in the GnomAD database, including 38,585 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 0.71 (38585 hom., cov: 34)
• Consequence: LOC105378590 XR_001737845.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71

Genes affected

LOC105378590 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378590	XR_001737845.3	n.696G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105378590	XR_007065356.1	n.983G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105378590	XR_007065357.1	n.983G>A		non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108101 AN: 152090 Hom.: 38563 Cov.: 34

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.711 AC: 108173 AN: 152208 Hom.: 38585 Cov.: 34 AF XY: 0.711 AC XY: 52937 AN XY: 74422

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.658

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.739

Alfa AF: 0.729 Hom.: 36271

Bravo AF: 0.710

Asia WGS AF: 0.709 AC: 2471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.51
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2376803; hg19: chr1-1967954; COSMIC: COSV59916903;