rs1023890

Variant names:

• chr4-117780291-G-A
• rs1023890
• ENST00000755294.1:n.190+3610C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-117780291-G-A
• chr4-117780291-G-C
• chr4-117780291-G-T

Variant summary

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

The ENST00000755294.1(ENSG00000288921):​n.190+3610C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 151,762 control chromosomes in the GnomAD database, including 25,162 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 0.55 (25162 hom., cov: 32)
• Consequence: ENSG00000288921 ENST00000755294.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.306
• Publications: 8 publications found

Genes affected

ENSG00000288921 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.799 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
ENSG00000288921	ENST00000755294.1	n.190+3610C>T		intron_variant	Intron 2 of 5
ENSG00000288921	ENST00000755295.1	n.166+3610C>T		intron_variant	Intron 2 of 3
ENSG00000288921	ENST00000755296.1	n.156+3610C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83660 AN: 151644 Hom.: 25114 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.613

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.552 AC: 83770 AN: 151762 Hom.: 25162 Cov.: 32 AF XY: 0.551 AC XY: 40857 AN XY: 74162

African (AFR) AF: 0.807 AC: 33448 AN: 41470

American (AMR) AF: 0.546 AC: 8289 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1694 AN: 3464

East Asian (EAS) AF: 0.607 AC: 3129 AN: 5154

South Asian (SAS) AF: 0.418 AC: 2015 AN: 4824

European-Finnish (FIN) AF: 0.416 AC: 4384 AN: 10526

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28894 AN: 67826

Other (OTH) AF: 0.556 AC: 1170 AN: 2104

Alfa AF: 0.468 Hom.: 4994

Bravo AF: 0.580

Asia WGS AF: 0.508 AC: 1759 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.1
DANN	Benign	0.69
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1023890; hg19: chr4-118701446;