1-234879452-C-T

Position:

• chr1-234879452-C-T

Variant summary

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

The ENST00000651370.1(ENSG00000286263):​n.185+53017G>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 0.791 in 152,104 control chromosomes in the GnomAD database, including 48,469 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 0.79 (48469 hom., cov: 31)
• Consequence: ENST00000651370.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 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
	ENST00000651370.1	n.185+53017G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.791 AC: 120232 AN: 151986 Hom.: 48405 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.718

Gnomad EAS AF: 0.945

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.769

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

GnomAD4 genome AF: 0.791 AC: 120358 AN: 152104 Hom.: 48469 Cov.: 31 AF XY: 0.789 AC XY: 58668 AN XY: 74338

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.812

Gnomad4 ASJ AF: 0.718

Gnomad4 EAS AF: 0.945

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.773

Alfa AF: 0.734 Hom.: 54095

Bravo AF: 0.814

Asia WGS AF: 0.896 AC: 3114 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2802955; hg19: chr1-235015199; COSMIC: COSV70148404;