1-55342470-C-T

Position:

• chr1-55342470-C-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, non coding transcript 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: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000643167.1	n.138+13045C>T		intron_variant, non_coding_transcript_variant

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;