rs11585386

Variant names:

• chr1-228883401-C-T
• rs11585386
• ENST00000848621.1:n.73-27905C>T

Variant summary

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

The ENST00000848621.1(ENSG00000310264):​n.73-27905C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.057 in 152,318 control chromosomes in the GnomAD database, including 349 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 0.057 (349 hom., cov: 32)
• Consequence: ENSG00000310264 ENST00000848621.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.406
• Publications: 7 publications found

Genes affected

ENSG00000310264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.088 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
ENSG00000310264	ENST00000848621.1	n.73-27905C>T		intron_variant	Intron 1 of 3
ENSG00000310285	ENST00000848808.1	n.213-24664G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0571 AC: 8686 AN: 152200 Hom.: 349 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0413

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0810

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0899

Gnomad OTH AF: 0.0507

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

GnomAD4 genome AF: 0.0570 AC: 8685 AN: 152318 Hom.: 349 Cov.: 32 AF XY: 0.0536 AC XY: 3995 AN XY: 74472

African (AFR) AF: 0.0167 AC: 696 AN: 41582

American (AMR) AF: 0.0412 AC: 631 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5178

South Asian (SAS) AF: 0.0101 AC: 49 AN: 4830

European-Finnish (FIN) AF: 0.0810 AC: 859 AN: 10610

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0899 AC: 6114 AN: 68020

Other (OTH) AF: 0.0501 AC: 106 AN: 2114

Alfa AF: 0.0746 Hom.: 1080

Bravo AF: 0.0516

Asia WGS AF: 0.00779 AC: 27 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.57
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs11585386; hg19: chr1-229019148;