1-55369757-C-T

Position:

• chr1-55369757-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+40332C>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 0.614 in 152,024 control chromosomes in the GnomAD database, including 28,793 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 0.61 (28793 hom., cov: 31)
• Consequence: ENST00000643167.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.572

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.641 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+40332C>T		intron_variant, non_coding_transcript_variant
	ENST00000646341.1	n.158+8192C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93353 AN: 151906 Hom.: 28773 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.614 AC: 93414 AN: 152024 Hom.: 28793 Cov.: 31 AF XY: 0.613 AC XY: 45516 AN XY: 74310

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.660

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.591

Alfa AF: 0.559 Hom.: 2821

Bravo AF: 0.605

Asia WGS AF: 0.620 AC: 2161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.3
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12565257; hg19: chr1-55835430; COSMIC: COSV70432393;