rs4798812

chr18-9420506-G-Achr18-9420506-G-T

Variant summary

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

The XR_001753550.2(LOC105371980):n.544-315G>A 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 0.296 in 152,028 control chromosomes in the GnomAD database, including 7,011 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 0.30 (7011 hom., cov: 32)
• Consequence: LOC105371980 XR_001753550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

Genes affected

LOC105371980 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371980	XR_001753550.2	n.544-315G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44980 AN: 151910 Hom.: 6996 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.296 AC: 45031 AN: 152028 Hom.: 7011 Cov.: 32 AF XY: 0.296 AC XY: 21976 AN XY: 74326

Gnomad4 AFR AF: 0.238

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.218

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.315

Alfa AF: 0.314 Hom.: 11526

Bravo AF: 0.315

Asia WGS AF: 0.355 AC: 1232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.0
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4798812; hg19: chr18-9420504;