chr10-77783319-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000228748 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434097.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228748	ENST00000434097.2	TSL:1	n.454G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000228748	ENST00000600739.2	TSL:6	n.529G>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000228748	ENST00000819302.1		n.466G>A		non_coding_transcript_exon	Exon 1 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.667 AC: 4 AN: 6

Other (OTH) AF: 0.500 AC: 1 AN: 2

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

African (AFR) AF: 0.916 AC: 38073 AN: 41552

American (AMR) AF: 0.764 AC: 11662 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2322 AN: 3472

East Asian (EAS) AF: 0.736 AC: 3815 AN: 5184

South Asian (SAS) AF: 0.680 AC: 3277 AN: 4820

European-Finnish (FIN) AF: 0.611 AC: 6447 AN: 10554

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.668 AC: 45374 AN: 67972

Other (OTH) AF: 0.726 AC: 1533 AN: 2112

Alfa AF: 0.687 Hom.: 11633

Bravo AF: 0.764

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.42
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs2579159; hg19: chr10-79543077;