18-55863647-A-T

Position:

• chr18-55863647-A-T

Variant summary

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

The XR_002958213.2(LOC105372131):​n.328+334A>T 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 0.618 in 151,990 control chromosomes in the GnomAD database, including 29,560 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 0.62 (29560 hom., cov: 32)
• Consequence: LOC105372131 XR_002958213.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.44

Genes affected

LOC105372131 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105372131	XR_002958213.2	n.328+334A>T		intron_variant, non_coding_transcript_variant
LOC105372131	XR_935495.4	n.182+114A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93909 AN: 151872 Hom.: 29549 Cov.: 32

Gnomad AFR AF: 0.570

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.618 AC: 93957 AN: 151990 Hom.: 29560 Cov.: 32 AF XY: 0.627 AC XY: 46572 AN XY: 74286

Gnomad4 AFR AF: 0.570

Gnomad4 AMR AF: 0.613

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.985

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.594

Gnomad4 OTH AF: 0.628

Alfa AF: 0.598 Hom.: 3380

Bravo AF: 0.612

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	19
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9675567; hg19: chr18-53530878;