rs2579159

chr10-77783319-G-Achr10-77783319-G-T

Variant summary

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

The ENST00000434097.2(ENSG00000228748):n.454G>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 0.745 in 152,152 control chromosomes in the GnomAD database, including 43,166 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 0.74 (43164 hom., cov: 32)
  • Exomes 𝑓: 0.67 (2 hom.)
• Consequence: ENST00000434097.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 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
	ENST00000434097.2	n.454G>A		non_coding_transcript_exon_variant	1/2	1
	ENST00000600739.1	n.154G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113156 AN: 152022 Hom.: 43105 Cov.: 32

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.642

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.611

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.724

GnomAD4 exome AF: 0.667 AC: 8 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.625 AC XY: 5 AN XY: 8

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.745 AC: 113275 AN: 152140 Hom.: 43164 Cov.: 32 AF XY: 0.740 AC XY: 55063 AN XY: 74368

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.669

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.611

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.726

Alfa AF: 0.689 Hom.: 9819

Bravo AF: 0.764

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	3.2
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2579159; hg19: chr10-79543077;