chr1-55647101-C-T

Position:

• chr1-55647101-C-T

Variant summary

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

The ENST00000643167.1(ENSG00000234810):​n.221-26159C>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 0.56 in 152,160 control chromosomes in the GnomAD database, including 24,826 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 0.56 (24826 hom., cov: 33)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 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.221-26159C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85123 AN: 152042 Hom.: 24817 Cov.: 33

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.560 AC: 85183 AN: 152160 Hom.: 24826 Cov.: 33 AF XY: 0.561 AC XY: 41754 AN XY: 74384

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.686

Gnomad4 ASJ AF: 0.562

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.560

Alfa AF: 0.584 Hom.: 35166

Bravo AF: 0.564

Asia WGS AF: 0.586 AC: 2037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10443215; hg19: chr1-56112774;