rs3860300

Positions:

• chr1-206891573-C-G

Variant summary

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

The XR_007066835.1(LOC105372879):​n.238G>C 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 0.47 in 152,006 control chromosomes in the GnomAD database, including 17,407 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 0.47 (17407 hom., cov: 32)
• Consequence: LOC105372879 XR_007066835.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

Genes affected

LOC105372879 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372879	XR_007066835.1	n.238G>C		non_coding_transcript_exon_variant	2/2
LOC105372879	XR_007066836.1	n.125+4421G>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71420 AN: 151888 Hom.: 17386 Cov.: 32

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.470 AC: 71503 AN: 152006 Hom.: 17407 Cov.: 32 AF XY: 0.462 AC XY: 34296 AN XY: 74306

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.456

Gnomad4 OTH AF: 0.498

Alfa AF: 0.469 Hom.: 2088

Bravo AF: 0.483

Asia WGS AF: 0.277 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.62
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3860300; hg19: chr1-207064918;