rs1011726

Variant names:

• chr1-190951337-G-A
• rs1011726
• ENST00000648197.1:n.735+25083C>T

Variant summary

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

The ENST00000648197.1(ENSG00000285638):​n.735+25083C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,504 control chromosomes in the GnomAD database, including 10,763 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 0.37 (10763 hom., cov: 31)
• Consequence: ENSG00000285638 ENST00000648197.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.513

Genes affected

ENSG00000285638 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 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
ENSG00000285638	ENST00000648197.1	n.735+25083C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56034 AN: 151386 Hom.: 10759 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.370 AC: 56049 AN: 151504 Hom.: 10763 Cov.: 31 AF XY: 0.370 AC XY: 27406 AN XY: 74028

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.508

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.369

Alfa AF: 0.397 Hom.: 9707

Bravo AF: 0.363

Asia WGS AF: 0.478 AC: 1659 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1011726; hg19: chr1-190920467;