rs4800820

Positions:

• chr18-27796509-C-T

Variant summary

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

The XR_935323.3(LOC105372042):​n.695+5247C>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 0.54 in 151,970 control chromosomes in the GnomAD database, including 24,566 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 0.54 (24566 hom., cov: 33)
• Consequence: LOC105372042 XR_935323.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241

Genes affected

LOC105372042 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.65 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372042	XR_935323.3	n.695+5247C>T		intron_variant, non_coding_transcript_variant
LOC105372042	XR_935324.3	n.628-6412C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82072 AN: 151852 Hom.: 24560 Cov.: 33

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.540 AC: 82095 AN: 151970 Hom.: 24566 Cov.: 33 AF XY: 0.545 AC XY: 40464 AN XY: 74268

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.595

Gnomad4 EAS AF: 0.466

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.655

Gnomad4 OTH AF: 0.552

Alfa AF: 0.636 Hom.: 63208

Bravo AF: 0.522

Asia WGS AF: 0.510 AC: 1772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800820; hg19: chr18-25376473; COSMIC: COSV69621225;