XR_935142.4:n.1633A>G

Variant names:

• chr18-10424832-A-G
• rs206503
• XR_935142.4:n.1633A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_935142.4(LOC105371988):​n.1633A>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 0.685 in 152,084 control chromosomes in the GnomAD database, including 36,506 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 0.68 (36506 hom., cov: 32)
• Consequence: LOC105371988 XR_935142.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 1 publications found

Genes affected

LOC105371988 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104054 AN: 151966 Hom.: 36487 Cov.: 32

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.721

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.685 AC: 104125 AN: 152084 Hom.: 36506 Cov.: 32 AF XY: 0.694 AC XY: 51581 AN XY: 74350

African (AFR) AF: 0.534 AC: 22143 AN: 41452

American (AMR) AF: 0.779 AC: 11913 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2182 AN: 3468

East Asian (EAS) AF: 0.854 AC: 4413 AN: 5168

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4812

European-Finnish (FIN) AF: 0.839 AC: 8880 AN: 10590

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.721 AC: 49009 AN: 67982

Other (OTH) AF: 0.672 AC: 1419 AN: 2112

Alfa AF: 0.708 Hom.: 89628

Bravo AF: 0.677

Asia WGS AF: 0.755 AC: 2628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.011
DANN	Benign	0.20
PhyloP100		-2.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs206503; hg19: chr18-10424829;