rs1875518

Positions:

• chr3-117510933-A-G
• chr3-117510933-A-T

Variant summary

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

The XR_924361.3(LOC105374056):​n.27613A>G 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 0.403 in 152,090 control chromosomes in the GnomAD database, including 15,044 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 0.40 (15044 hom., cov: 32)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

LOC105374056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105374056	XR_007096021.1	n.27613A>G		non_coding_transcript_exon_variant	1/3
LOC105374056	XR_924361.3	n.27613A>G		non_coding_transcript_exon_variant	1/4
		n.117510933A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61352 AN: 151972 Hom.: 15052 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.403 AC: 61325 AN: 152090 Hom.: 15044 Cov.: 32 AF XY: 0.399 AC XY: 29683 AN XY: 74334

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.417

Alfa AF: 0.475 Hom.: 2395

Bravo AF: 0.377

Asia WGS AF: 0.355 AC: 1236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.3
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1875518; hg19: chr3-117229780;