rs2579159

Variant names:

• chr10-77783319-G-A
• rs2579159
• ENST00000434097.2:n.454G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-77783319-G-A
• chr10-77783319-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: ENSG00000228748 ENST00000434097.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

ENSG00000228748 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228748	ENST00000434097.2	n.454G>A		non_coding_transcript_exon_variant	Exon 1 of 2	1
ENSG00000228748	ENST00000600739.1	n.154G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;