chr1-234927823-C-A

Position:

• chr1-234927823-C-A

Variant summary

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

The ENST00000651370.1(ENSG00000286263):​n.185+4646G>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 0.13 in 152,114 control chromosomes in the GnomAD database, including 1,489 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 0.13 (1489 hom., cov: 31)
• Consequence: ENST00000651370.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 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+4646G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19803 AN: 151996 Hom.: 1490 Cov.: 31

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0850

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0711

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.130 AC: 19807 AN: 152114 Hom.: 1489 Cov.: 31 AF XY: 0.132 AC XY: 9826 AN XY: 74390

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0847

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0712

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.112

Alfa AF: 0.156 Hom.: 327

Bravo AF: 0.114

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12133603; hg19: chr1-235063570;