1-55773588-T-A

Position:

• chr1-55773588-T-A

Variant summary

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

The ENST00000643167.1(ENSG00000234810):​n.279-58676T>A 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 0.489 in 152,024 control chromosomes in the GnomAD database, including 18,582 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 0.49 (18582 hom., cov: 33)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.669 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.279-58676T>A		intron_variant, non_coding_transcript_variant
	ENST00000634769.1	n.275-58676T>A		intron_variant, non_coding_transcript_variant		5
	ENST00000646341.1	n.299-58676T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.489 AC: 74310 AN: 151906 Hom.: 18570 Cov.: 33

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.489 AC: 74357 AN: 152024 Hom.: 18582 Cov.: 33 AF XY: 0.491 AC XY: 36500 AN XY: 74302

Gnomad4 AFR AF: 0.579

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.493

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.478

Alfa AF: 0.315 Hom.: 760

Bravo AF: 0.483

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs753978; hg19: chr1-56239261;