rs952146

Variant names:

• chr1-154396452-A-G
• rs952146
• ENST00000745817.1:n.211+5246T>C

Variant summary

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

The ENST00000745817.1(ENSG00000297143):​n.211+5246T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,040 control chromosomes in the GnomAD database, including 11,510 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 0.39 (11510 hom., cov: 32)
• Consequence: ENSG00000297143 ENST00000745817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250
• Publications: 16 publications found

Genes affected

ENSG00000297143 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.408 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
ENSG00000297143	ENST00000745817.1	n.211+5246T>C		intron_variant	Intron 1 of 1
ENSG00000297143	ENST00000745818.1	n.216-4570T>C		intron_variant	Intron 1 of 1
ENSG00000297143	ENST00000745819.1	n.84-4600T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58633 AN: 151920 Hom.: 11483 Cov.: 32

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.386 AC: 58699 AN: 152040 Hom.: 11510 Cov.: 32 AF XY: 0.385 AC XY: 28619 AN XY: 74312

African (AFR) AF: 0.413 AC: 17123 AN: 41470

American (AMR) AF: 0.366 AC: 5583 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3470

East Asian (EAS) AF: 0.299 AC: 1544 AN: 5164

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4820

European-Finnish (FIN) AF: 0.440 AC: 4642 AN: 10560

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26130 AN: 67978

Other (OTH) AF: 0.362 AC: 764 AN: 2112

Alfa AF: 0.382 Hom.: 29551

Bravo AF: 0.381

Asia WGS AF: 0.294 AC: 1027 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	4.9
DANN	Benign	0.75
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs952146; hg19: chr1-154368928;