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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371988	XR_935142.4	n.1633A>G		non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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

Other links and lift over

dbSNP: rs206503; hg19: chr18-10424829;