rs10002492

Variant names:

• chr4-12578222-A-G
• rs10002492
• ENST00000808833.1:n.347+31120T>C

Variant summary

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

The ENST00000808833.1(ENSG00000305112):​n.347+31120T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,048 control chromosomes in the GnomAD database, including 5,119 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 0.21 (5119 hom., cov: 32)
• Consequence: ENSG00000305112 ENST00000808833.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 1 publications found

Genes affected

ENSG00000305112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808833.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305112	ENST00000808833.1		n.347+31120T>C		intron	N/A
	ENSG00000305112	ENST00000808834.1		n.71-3057T>C		intron	N/A
	ENSG00000305112	ENST00000808835.1		n.351+31120T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32599 AN: 151932 Hom.: 5097 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0281

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.215 AC: 32659 AN: 152048 Hom.: 5119 Cov.: 32 AF XY: 0.209 AC XY: 15547 AN XY: 74298

African (AFR) AF: 0.450 AC: 18621 AN: 41420

American (AMR) AF: 0.117 AC: 1784 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3468

East Asian (EAS) AF: 0.0282 AC: 146 AN: 5182

South Asian (SAS) AF: 0.119 AC: 575 AN: 4812

European-Finnish (FIN) AF: 0.106 AC: 1126 AN: 10594

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9319 AN: 67978

Other (OTH) AF: 0.190 AC: 401 AN: 2116

Alfa AF: 0.172 Hom.: 4627

Bravo AF: 0.223

Asia WGS AF: 0.0980 AC: 341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.59
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10002492; hg19: chr4-12579846;