18-70486384-T-C

Position:

• chr18-70486384-T-C

Variant summary

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

The XR_935606.3(LOC105376872):​n.227T>C 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 0.74 in 152,144 control chromosomes in the GnomAD database, including 43,907 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 0.74 (43907 hom., cov: 33)
• Consequence: LOC105376872 XR_935606.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10

Genes affected

LOC105376872 (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 (EAS) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376872	XR_935606.3	n.227T>C		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000687285.1	n.123+21345T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.741 AC: 112583 AN: 152026 Hom.: 43883 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.895

Gnomad SAS AF: 0.795

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.740 AC: 112645 AN: 152144 Hom.: 43907 Cov.: 33 AF XY: 0.747 AC XY: 55544 AN XY: 74378

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.766

Alfa AF: 0.832 Hom.: 91600

Bravo AF: 0.725

Asia WGS AF: 0.814 AC: 2833 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	7.0
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11663206; hg19: chr18-68153620;