rs1876040

Positions:

• chr2-18953470-A-G
• chr2-18953470-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007086234.1(LOC105373456):​n.1138+34093A>G 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 0.0496 in 152,314 control chromosomes in the GnomAD database, including 680 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 (680 hom., cov: 32)
• Consequence: LOC105373456 XR_007086234.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30

Genes affected

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373456	XR_007086234.1	n.1138+34093A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0496 AC: 7556 AN: 152194 Hom.: 679 Cov.: 32

Gnomad AFR AF: 0.00909

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0496 AC: 7549 AN: 152314 Hom.: 680 Cov.: 32 AF XY: 0.0554 AC XY: 4125 AN XY: 74468

Gnomad4 AFR AF: 0.00907

Gnomad4 AMR AF: 0.0589

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.0336

Gnomad4 OTH AF: 0.0487

Alfa AF: 0.0481 Hom.: 1206

Bravo AF: 0.0491

Asia WGS AF: 0.248 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	16
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1876040; hg19: chr2-19134748;