rs948716

chr18-77452299-T-C

Variant summary

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

The ENST00000583629.2(ENSG00000264015):n.406+30275T>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 0.211 in 152,136 control chromosomes in the GnomAD database, including 4,183 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 0.21 (4183 hom., cov: 32)
• Consequence: ENST00000583629.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83

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 (AFR) allele frequency at 95% confidence interval = 0.356 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
	ENST00000583629.2	n.406+30275T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32083 AN: 152018 Hom.: 4171 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.211 AC: 32139 AN: 152136 Hom.: 4183 Cov.: 32 AF XY: 0.212 AC XY: 15778 AN XY: 74368

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.216

Alfa AF: 0.182 Hom.: 498

Bravo AF: 0.218

Asia WGS AF: 0.171 AC: 594 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	0.16
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs948716; hg19: chr18-75164255;