rs899101

Positions:

• chr18-55788000-T-C

Variant summary

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

The ENST00000654829.1(ENSG00000267284):​n.304-613T>C 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 0.263 in 152,178 control chromosomes in the GnomAD database, including 5,829 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 0.26 (5829 hom., cov: 33)
• Consequence: ENST00000654829.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372130	XR_007066382.1	n.476-613T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654829.1	n.304-613T>C		intron_variant, non_coding_transcript_variant
	ENST00000589662.1	n.365-613T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39978 AN: 152060 Hom.: 5823 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.263 AC: 40024 AN: 152178 Hom.: 5829 Cov.: 33 AF XY: 0.262 AC XY: 19526 AN XY: 74404

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.271

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.268

Alfa AF: 0.269 Hom.: 827

Bravo AF: 0.267

Asia WGS AF: 0.210 AC: 729 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	0.48
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs899101; hg19: chr18-53455231;