1-156689976-C-T

Position:

• chr1-156689976-C-T

Variant summary

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

The ENST00000441272.2(ENSG00000237588):​n.1841G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.699 in 152,174 control chromosomes in the GnomAD database, including 37,290 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 0.70 (37256 hom., cov: 31)
  • Exomes 𝑓: 0.71 (34 hom.)
• Consequence: ENST00000441272.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

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 (AFR) allele frequency at 95% confidence interval = 0.745 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
	ENST00000441272.2	n.1841G>A		non_coding_transcript_exon_variant	2/2	5
	ENST00000650347.1	n.149+152C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.699 AC: 106151 AN: 151920 Hom.: 37224 Cov.: 31

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.662

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.666

GnomAD4 exome AF: 0.706 AC: 96 AN: 136 Hom.: 34 Cov.: 0 AF XY: 0.693 AC XY: 79 AN XY: 114

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.739

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.699 AC: 106234 AN: 152038 Hom.: 37256 Cov.: 31 AF XY: 0.700 AC XY: 52058 AN XY: 74320

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.662

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.661

Alfa AF: 0.676 Hom.: 66941

Bravo AF: 0.698

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7532302; hg19: chr1-156659768;