1-55342470-C-T

Variant names:

• chr1-55342470-C-T
• rs207145
• ENST00000643167.1:n.138+13045C>T

Variant summary

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

The ENST00000643167.1(ENSG00000234810):​n.138+13045C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.901 in 152,252 control chromosomes in the GnomAD database, including 61,917 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 0.90 (61917 hom., cov: 32)
• Consequence: ENSG00000234810 ENST00000643167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

ENSG00000234810 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 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
ENSG00000234810	ENST00000643167.1	n.138+13045C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.901 AC: 137078 AN: 152134 Hom.: 61873 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.834

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.877

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.901 AC: 137183 AN: 152252 Hom.: 61917 Cov.: 32 AF XY: 0.902 AC XY: 67139 AN XY: 74432

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.907

Gnomad4 ASJ AF: 0.834

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.924

Gnomad4 FIN AF: 0.884

Gnomad4 NFE AF: 0.877

Gnomad4 OTH AF: 0.892

Alfa AF: 0.889 Hom.: 28673

Bravo AF: 0.903

Asia WGS AF: 0.898 AC: 3122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.3
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs207145; hg19: chr1-55808143;