1-193952418-C-T

Variant names:

• chr1-193952418-C-T
• rs606149
• ENST00000656143.2:n.378+53051C>T

Variant summary

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

The ENST00000656143.2(ENSG00000227240):​n.378+53051C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.381 in 152,082 control chromosomes in the GnomAD database, including 13,452 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 0.38 (13452 hom., cov: 32)
• Consequence: ENSG00000227240 ENST00000656143.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 14 publications found

Genes affected

ENSG00000227240 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904475	XR_007066777.1	n.5412+53051C>T		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227240	ENST00000656143.2	n.378+53051C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.382 AC: 57994 AN: 151964 Hom.: 13462 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.721

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.381 AC: 57982 AN: 152082 Hom.: 13452 Cov.: 32 AF XY: 0.388 AC XY: 28873 AN XY: 74322

African (AFR) AF: 0.118 AC: 4913 AN: 41508

American (AMR) AF: 0.507 AC: 7753 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1688 AN: 3472

East Asian (EAS) AF: 0.721 AC: 3724 AN: 5162

South Asian (SAS) AF: 0.605 AC: 2917 AN: 4822

European-Finnish (FIN) AF: 0.441 AC: 4663 AN: 10568

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30733 AN: 67954

Other (OTH) AF: 0.425 AC: 897 AN: 2110

Alfa AF: 0.440 Hom.: 64734

Bravo AF: 0.375

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.72
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs606149; hg19: chr1-193921548;