18-38483901-T-C

Position:

• chr18-38483901-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_935392.1(LOC105372074):​n.204+6180A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 151,808 control chromosomes in the GnomAD database, including 51,732 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 0.82 (51732 hom., cov: 29)
• Consequence: LOC105372074 XR_935392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

Genes affected

LOC105372074 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372074	XR_935392.1	n.204+6180A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124146 AN: 151690 Hom.: 51708 Cov.: 29

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.856

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.818 AC: 124228 AN: 151808 Hom.: 51732 Cov.: 29 AF XY: 0.817 AC XY: 60639 AN XY: 74178

Gnomad4 AFR AF: 0.662

Gnomad4 AMR AF: 0.850

Gnomad4 ASJ AF: 0.856

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.906

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.833

Alfa AF: 0.888 Hom.: 96628

Bravo AF: 0.805

Asia WGS AF: 0.691 AC: 2405 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	19
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1365463; hg19: chr18-36063865;