rs2368416

Variant names:

• chr10-29408056-T-C
• rs2368416
• ENST00000658254.1:n.1122+189A>G

Your query was ambiguous. Multiple possible variants found:

• chr10-29408056-T-C
• chr10-29408056-T-G

Variant summary

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

The ENST00000658254.1(ENSG00000287402):​n.1122+189A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,412 control chromosomes in the GnomAD database, including 20,929 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 0.52 (20929 hom., cov: 30)
• Consequence: ENSG00000287402 ENST00000658254.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 3 publications found

Genes affected

ENSG00000287402 (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 (AFR) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658254.1. 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
	ENSG00000287402	ENST00000658254.1		n.1122+189A>G		intron	N/A
	ENSG00000287402	ENST00000729529.1		n.504+189A>G		intron	N/A
	ENSG00000287402	ENST00000729530.1		n.491+189A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78048 AN: 151294 Hom.: 20881 Cov.: 30

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.577

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.516 AC: 78157 AN: 151412 Hom.: 20929 Cov.: 30 AF XY: 0.524 AC XY: 38718 AN XY: 73892

African (AFR) AF: 0.626 AC: 25810 AN: 41246

American (AMR) AF: 0.573 AC: 8701 AN: 15188

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1105 AN: 3464

East Asian (EAS) AF: 0.577 AC: 2969 AN: 5142

South Asian (SAS) AF: 0.458 AC: 2195 AN: 4790

European-Finnish (FIN) AF: 0.566 AC: 5896 AN: 10408

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.443 AC: 30033 AN: 67864

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.503 Hom.: 3410

Bravo AF: 0.523

Asia WGS AF: 0.490 AC: 1700 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	2.0
DANN	Benign	0.20
PhyloP100		-0.93

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: rs2368416;

hg19: chr10-29696985;