rs2023890

Variant names:

• chr7-24293128-G-A
• rs2023890
• ENST00000718234.1:n.319+26229C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-24293128-G-A
• chr7-24293128-G-C

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+26229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.767 in 152,156 control chromosomes in the GnomAD database, including 45,017 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 0.77 (45017 hom., cov: 31)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 8 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.916 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000228944	ENST00000718234.1		n.319+26229C>T		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+26229C>T		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+26229C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116586 AN: 152038 Hom.: 44992 Cov.: 31

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.767 AC: 116659 AN: 152156 Hom.: 45017 Cov.: 31 AF XY: 0.771 AC XY: 57331 AN XY: 74392

African (AFR) AF: 0.694 AC: 28792 AN: 41492

American (AMR) AF: 0.830 AC: 12693 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2809 AN: 3468

East Asian (EAS) AF: 0.938 AC: 4861 AN: 5180

South Asian (SAS) AF: 0.857 AC: 4136 AN: 4828

European-Finnish (FIN) AF: 0.767 AC: 8127 AN: 10592

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.773 AC: 52558 AN: 67986

Other (OTH) AF: 0.786 AC: 1663 AN: 2116

Alfa AF: 0.770 Hom.: 5642

Bravo AF: 0.767

Asia WGS AF: 0.857 AC: 2980 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.38
PhyloP100		-0.54

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2023890;

hg19: chr7-24332747;