rs10789336

Positions:

• chr1-72372723-G-A
• chr1-72372723-G-C

Variant summary

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

The ENST00000653965.1(ENSG00000286863):​n.236+89318G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 151,982 control chromosomes in the GnomAD database, including 29,816 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 0.62 (29816 hom., cov: 31)
• Consequence: ENSG00000286863 ENST00000653965.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147

Genes affected

ENSG00000286863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378797	XR_001737670.2	n.472+89318G>A		intron_variant
LOC105378797	XR_001737671.3	n.472+89318G>A		intron_variant
LOC105378797	XR_947505.3	n.472+89318G>A		intron_variant
LOC105378797	XR_947506.3	n.472+89318G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286863	ENST00000653965.1	n.236+89318G>A		intron_variant
ENSG00000286863	ENST00000665984.1	n.153+89318G>A		intron_variant
ENSG00000286863	ENST00000667836.1	n.227+89318G>A		intron_variant
ENSG00000286863	ENST00000688733.1	n.56+89318G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94149 AN: 151864 Hom.: 29802 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.620 AC: 94197 AN: 151982 Hom.: 29816 Cov.: 31 AF XY: 0.627 AC XY: 46569 AN XY: 74276

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.647

Alfa AF: 0.613 Hom.: 3543

Bravo AF: 0.623

Asia WGS AF: 0.751 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10789336; hg19: chr1-72838406;