10-5289196-A-G

Variant names:

• chr10-5289196-A-G
• rs2398236
• ENST00000744973.1:n.142+2512T>C

Variant summary

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

The ENST00000744973.1(ENSG00000291045):​n.142+2512T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 152,144 control chromosomes in the GnomAD database, including 31,130 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 0.64 (31130 hom., cov: 33)
• Consequence: ENSG00000291045 ENST00000744973.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190
• Publications: 4 publications found

Genes affected

ENSG00000291045 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744973.1. 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
	ENSG00000291045	ENST00000744973.1		n.142+2512T>C		intron	N/A
	ENSG00000291045	ENST00000744974.1		n.107+2600T>C		intron	N/A
	ENSG00000291045	ENST00000744975.1		n.190+2512T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96738 AN: 152026 Hom.: 31098 Cov.: 33

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.576

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.636 AC: 96827 AN: 152144 Hom.: 31130 Cov.: 33 AF XY: 0.639 AC XY: 47534 AN XY: 74380

African (AFR) AF: 0.696 AC: 28891 AN: 41492

American (AMR) AF: 0.577 AC: 8819 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2084 AN: 3470

East Asian (EAS) AF: 0.756 AC: 3917 AN: 5184

South Asian (SAS) AF: 0.763 AC: 3682 AN: 4824

European-Finnish (FIN) AF: 0.603 AC: 6377 AN: 10582

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.602 AC: 40957 AN: 67988

Other (OTH) AF: 0.610 AC: 1288 AN: 2112

Alfa AF: 0.617 Hom.: 14383

Bravo AF: 0.633

Asia WGS AF: 0.770 AC: 2678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.58
PhyloP100		-0.19

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: rs2398236;

hg19: chr10-5331159;