1-111320684-C-T

Position:

• chr1-111320684-C-T

Variant summary

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

The ENST00000426321.1(ENSG00000229283):​n.149-2757G>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 0.129 in 570,792 control chromosomes in the GnomAD database, including 6,079 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 0.16 (2765 hom., cov: 32)
  • Exomes 𝑓: 0.12 (3314 hom.)
• Consequence: ENST00000426321.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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
	ENST00000426321.1	n.149-2757G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24938 AN: 151896 Hom.: 2761 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0985

Gnomad ASJ AF: 0.0812

Gnomad EAS AF: 0.0955

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.136

GnomAD4 exome AF: 0.116 AC: 48732 AN: 418778 Hom.: 3314 AF XY: 0.118 AC XY: 25793 AN XY: 218952

Gnomad4 AFR exome AF: 0.322

Gnomad4 AMR exome AF: 0.0771

Gnomad4 ASJ exome AF: 0.0805

Gnomad4 EAS exome AF: 0.0835

Gnomad4 SAS exome AF: 0.157

Gnomad4 FIN exome AF: 0.0839

Gnomad4 NFE exome AF: 0.112

Gnomad4 OTH exome AF: 0.117

GnomAD4 genome AF: 0.164 AC: 24973 AN: 152014 Hom.: 2765 Cov.: 32 AF XY: 0.162 AC XY: 12076 AN XY: 74338

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.0981

Gnomad4 ASJ AF: 0.0812

Gnomad4 EAS AF: 0.0957

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.136

Alfa AF: 0.127 Hom.: 721

Bravo AF: 0.169

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.64
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2820093; hg19: chr1-111863306;