chr8-8933743-C-A

Position:

• chr8-8933743-C-A

Variant summary

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

The ENST00000603391.1(ENSG00000270966):​n.264G>T 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 0.584 in 1,312,058 control chromosomes in the GnomAD database, including 231,862 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 0.57 (25896 hom., cov: 31)
  • Exomes 𝑓: 0.59 (205966 hom.)
• Consequence: ENST00000603391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 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
	ENST00000603391.1	n.264G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86513 AN: 151770 Hom.: 25854 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.650

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.582

GnomAD4 exome AF: 0.586 AC: 679479 AN: 1160170 Hom.: 205966 Cov.: 18 AF XY: 0.580 AC XY: 342966 AN XY: 591060

Gnomad4 AFR exome AF: 0.747

Gnomad4 AMR exome AF: 0.284

Gnomad4 ASJ exome AF: 0.651

Gnomad4 EAS exome AF: 0.227

Gnomad4 SAS exome AF: 0.481

Gnomad4 FIN exome AF: 0.546

Gnomad4 NFE exome AF: 0.622

Gnomad4 OTH exome AF: 0.588

GnomAD4 genome AF: 0.570 AC: 86602 AN: 151888 Hom.: 25896 Cov.: 31 AF XY: 0.559 AC XY: 41485 AN XY: 74202

Gnomad4 AFR AF: 0.705

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.650

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.584

Alfa AF: 0.595 Hom.: 3423

Bravo AF: 0.562

Asia WGS AF: 0.418 AC: 1458 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.49
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4841072; hg19: chr8-8791253;