rs2817056

Positions:

• chr6-35766274-C-A
• chr6-35766274-C-G
• chr6-35766274-C-T

Variant summary

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

The ENST00000403727.1(ENSG00000220734):​n.367C>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 0.551 in 281,436 control chromosomes in the GnomAD database, including 46,063 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 0.64 (31529 hom., cov: 31)
  • Exomes 𝑓: 0.45 (14534 hom.)
• Consequence: ENST00000403727.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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
	ENST00000403727.1	n.367C>A		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96994 AN: 151718 Hom.: 31498 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.672

GnomAD4 exome AF: 0.448 AC: 58110 AN: 129600 Hom.: 14534 Cov.: 0 AF XY: 0.450 AC XY: 33169 AN XY: 73698

Gnomad4 AFR exome AF: 0.469

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.562

Gnomad4 EAS exome AF: 0.230

Gnomad4 SAS exome AF: 0.547

Gnomad4 FIN exome AF: 0.421

Gnomad4 NFE exome AF: 0.443

Gnomad4 OTH exome AF: 0.481

GnomAD4 genome AF: 0.639 AC: 97068 AN: 151836 Hom.: 31529 Cov.: 31 AF XY: 0.637 AC XY: 47285 AN XY: 74206

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.713

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.674

Alfa AF: 0.613 Hom.: 58043

Bravo AF: 0.638

Asia WGS AF: 0.627 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2817056; hg19: chr6-35734051;