rs2419587

Variant names:

• chr10-111473405-C-T
• rs2419587
• ENST00000803672.1:n.377-4592C>T

Variant summary

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

The ENST00000803672.1(ENSG00000304475):​n.377-4592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 152,194 control chromosomes in the GnomAD database, including 1,141 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 0.073 (1141 hom., cov: 31)
• Consequence: ENSG00000304475 ENST00000803672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.262
• Publications: 0 publications found

Genes affected

ENSG00000304475 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803672.1. 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
	ENSG00000304475	ENST00000803672.1		n.377-4592C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10994 AN: 152076 Hom.: 1134 Cov.: 31

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0346

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.0226

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00639

Gnomad OTH AF: 0.0593

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

GnomAD4 genome AF: 0.0725 AC: 11040 AN: 152194 Hom.: 1141 Cov.: 31 AF XY: 0.0714 AC XY: 5317 AN XY: 74432

African (AFR) AF: 0.235 AC: 9735 AN: 41492

American (AMR) AF: 0.0345 AC: 528 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0219 AC: 76 AN: 3468

East Asian (EAS) AF: 0.00348 AC: 18 AN: 5176

South Asian (SAS) AF: 0.0222 AC: 107 AN: 4816

European-Finnish (FIN) AF: 0.000377 AC: 4 AN: 10612

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00640 AC: 435 AN: 68014

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0203 Hom.: 35

Bravo AF: 0.0819

Asia WGS AF: 0.0290 AC: 100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	8.5
DANN	Benign	0.87
PhyloP100		0.26

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: rs2419587;

hg19: chr10-113233163;