chr1-159563278-C-T

Variant names:

• chr1-159563278-C-T
• rs10908734
• ENST00000693113.1:n.754+13260G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693113.1(ENSG00000289484):​n.754+13260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.82 in 152,148 control chromosomes in the GnomAD database, including 52,047 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 0.82 (52047 hom., cov: 32)
• Consequence: ENSG00000289484 ENST00000693113.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 4 publications found

Genes affected

ENSG00000289484 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000693113.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289484	ENST00000693113.1		n.754+13260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.820 AC: 124713 AN: 152030 Hom.: 52024 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.895

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.876

Gnomad OTH AF: 0.849

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.820 AC: 124778 AN: 152148 Hom.: 52047 Cov.: 32 AF XY: 0.821 AC XY: 61064 AN XY: 74386

African (AFR) AF: 0.652 AC: 27039 AN: 41456

American (AMR) AF: 0.893 AC: 13659 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3194 AN: 3470

East Asian (EAS) AF: 0.986 AC: 5100 AN: 5172

South Asian (SAS) AF: 0.894 AC: 4313 AN: 4822

European-Finnish (FIN) AF: 0.852 AC: 9038 AN: 10612

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.876 AC: 59564 AN: 68002

Other (OTH) AF: 0.851 AC: 1798 AN: 2114

Alfa AF: 0.860 Hom.: 167769

Bravo AF: 0.817

Asia WGS AF: 0.912 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	0.86
DANN	Benign	0.47
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10908734; hg19: chr1-159533068;