rs4518838

chr1-46625477-T-C

Variant summary

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

The XR_947297.2(LOC105378697):n.345A>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 0.662 in 152,128 control chromosomes in the GnomAD database, including 34,449 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 0.66 (34449 hom., cov: 33)
• Consequence: LOC105378697 XR_947297.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

Genes affected

LOC105378697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378697	XR_947297.2	n.345A>G		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.662 AC: 100650 AN: 152010 Hom.: 34435 Cov.: 33

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.682

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.662 AC: 100705 AN: 152128 Hom.: 34449 Cov.: 33 AF XY: 0.654 AC XY: 48621 AN XY: 74352

Gnomad4 AFR AF: 0.573

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.177

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.659

Alfa AF: 0.714 Hom.: 16497

Bravo AF: 0.649

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.8
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4518838; hg19: chr1-47091149;