rs948716

Variant names:

• chr18-77452299-T-C
• rs948716
• ENST00000583629.2:n.406+30275T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000583629.2(ENSG00000264015):​n.406+30275T>C variant causes a intron 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: ENSG00000264015 ENST00000583629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.83
• Publications: 2 publications found

Genes affected

ENSG00000264015 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264015	ENST00000583629.2	n.406+30275T>C		intron_variant	Intron 1 of 2	4
ENSG00000264015	ENST00000744289.1	n.179+30275T>C		intron_variant	Intron 2 of 3
ENSG00000264015	ENST00000744290.1	n.495+30275T>C		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.361 AC: 14973 AN: 41488

American (AMR) AF: 0.197 AC: 3006 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3472

East Asian (EAS) AF: 0.122 AC: 629 AN: 5166

South Asian (SAS) AF: 0.198 AC: 955 AN: 4814

European-Finnish (FIN) AF: 0.155 AC: 1636 AN: 10588

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9322 AN: 68014

Other (OTH) AF: 0.216 AC: 456 AN: 2112

Alfa AF: 0.187 Hom.: 546

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs948716; hg19: chr18-75164255;