rs1891311

Variant names:

• chr10-90858859-A-G
• rs1891311
• ENST00000755194.1:n.266-203A>G

Variant summary

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

The ENST00000755194.1(ENSG00000298380):​n.266-203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,244 control chromosomes in the GnomAD database, including 1,473 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 0.12 (1473 hom., cov: 32)
• Consequence: ENSG00000298380 ENST00000755194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158
• Publications: 8 publications found

Genes affected

ENSG00000298380 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 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
ENSG00000298380	ENST00000755194.1	n.266-203A>G		intron_variant	Intron 1 of 2
ENSG00000298380	ENST00000755195.1	n.137-203A>G		intron_variant	Intron 1 of 2
ENSG00000298380	ENST00000755196.1	n.228-203A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18019 AN: 152126 Hom.: 1469 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0807

Gnomad ASJ AF: 0.0328

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0957

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0696

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.119 AC: 18043 AN: 152244 Hom.: 1473 Cov.: 32 AF XY: 0.118 AC XY: 8770 AN XY: 74444

African (AFR) AF: 0.227 AC: 9417 AN: 41502

American (AMR) AF: 0.0808 AC: 1236 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0328 AC: 114 AN: 3472

East Asian (EAS) AF: 0.157 AC: 814 AN: 5182

South Asian (SAS) AF: 0.0929 AC: 449 AN: 4832

European-Finnish (FIN) AF: 0.0957 AC: 1016 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0696 AC: 4733 AN: 68026

Other (OTH) AF: 0.106 AC: 224 AN: 2116

Alfa AF: 0.0932 Hom.: 1843

Bravo AF: 0.123

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.3
DANN	Benign	0.45
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs1891311; hg19: chr10-92618616;