rs299247

chr18-22709809-C-T

Variant summary

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

The ENST00000578831.1(ENSG00000265943):n.288-4889G>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 0.239 in 152,108 control chromosomes in the GnomAD database, including 6,417 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 0.24 (6417 hom., cov: 32)
• Consequence: ENST00000578831.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000578831.1	n.288-4889G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36302 AN: 151988 Hom.: 6387 Cov.: 32

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.0750

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.239 AC: 36385 AN: 152108 Hom.: 6417 Cov.: 32 AF XY: 0.238 AC XY: 17729 AN XY: 74366

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.0750

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.206

Alfa AF: 0.142 Hom.: 2567

Bravo AF: 0.258

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	15
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs299247; hg19: chr18-20289772;