rs1278527

Positions:

• chr1-50425295-T-C

Variant summary

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

The ENST00000641778.1(ENSG00000284700):​n.909T>C 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 0.471 in 152,280 control chromosomes in the GnomAD database, including 17,808 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 0.47 (17791 hom., cov: 33)
  • Exomes 𝑓: 0.49 (17 hom.)
• Consequence: ENST00000641778.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000641778.1	n.909T>C		non_coding_transcript_exon_variant	3/3
	ENST00000686764.1	n.757T>C		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71504 AN: 152022 Hom.: 17748 Cov.: 33

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.499

GnomAD4 exome AF: 0.486 AC: 68 AN: 140 Hom.: 17 Cov.: 0 AF XY: 0.455 AC XY: 51 AN XY: 112

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.492

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.471 AC: 71582 AN: 152140 Hom.: 17791 Cov.: 33 AF XY: 0.457 AC XY: 33991 AN XY: 74370

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.503

Alfa AF: 0.466 Hom.: 3415

Bravo AF: 0.482

Asia WGS AF: 0.333 AC: 1158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1278527; hg19: chr1-50890967;