XR_947297.2:n.345A>G

Variant names:

• chr1-46625477-T-C
• rs4518838
• XR_947297.2:n.345A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LOC105378697 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.573 AC: 23768 AN: 41474

American (AMR) AF: 0.605 AC: 9251 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2542 AN: 3472

East Asian (EAS) AF: 0.177 AC: 915 AN: 5170

South Asian (SAS) AF: 0.621 AC: 2997 AN: 4824

European-Finnish (FIN) AF: 0.721 AC: 7636 AN: 10584

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.753 AC: 51238 AN: 68004

Other (OTH) AF: 0.659 AC: 1393 AN: 2114

Alfa AF: 0.714 Hom.: 24910

Bravo AF: 0.649

Asia WGS AF: 0.436 AC: 1516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.82
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs4518838; hg19: chr1-47091149;