chr1-159563278-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000289484 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000289484	ENST00000693113.1	n.754+13260G>A		intron_variant	Intron 2 of 2

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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.852

Gnomad4 NFE AF: 0.876

Gnomad4 OTH AF: 0.851

Alfa AF: 0.872 Hom.: 74559

Bravo AF: 0.817

Asia WGS AF: 0.912 AC: 3169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908734; hg19: chr1-159533068;