rs10213502

Variant names:

• chr4-11947030-A-G
• rs10213502
• ENST00000824806.1:n.200+37642T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-11947030-A-G
• chr4-11947030-A-T

Variant summary

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

The ENST00000824806.1(ENSG00000307260):​n.200+37642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,544 control chromosomes in the GnomAD database, including 10,261 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 0.30 (10261 hom., cov: 30)
• Consequence: ENSG00000307260 ENST00000824806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.826
• Publications: 3 publications found

Genes affected

ENSG00000307260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824806.1. 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
	ENSG00000307260	ENST00000824806.1		n.200+37642T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46111 AN: 151426 Hom.: 10227 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0218

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.305 AC: 46187 AN: 151544 Hom.: 10261 Cov.: 30 AF XY: 0.297 AC XY: 22015 AN XY: 74008

African (AFR) AF: 0.633 AC: 26124 AN: 41244

American (AMR) AF: 0.205 AC: 3116 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.231 AC: 801 AN: 3466

East Asian (EAS) AF: 0.0220 AC: 113 AN: 5128

South Asian (SAS) AF: 0.186 AC: 894 AN: 4794

European-Finnish (FIN) AF: 0.143 AC: 1507 AN: 10524

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12728 AN: 67896

Other (OTH) AF: 0.272 AC: 572 AN: 2104

Alfa AF: 0.220 Hom.: 18424

Bravo AF: 0.323

Asia WGS AF: 0.134 AC: 468 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	1.4
DANN	Benign	0.42
PhyloP100		-0.83

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: rs10213502;

hg19: chr4-11948654;