rs3952812

Variant names:

• chr3-194090244-C-G
• rs3952812
• XM_011513352.4:c.280-1263C>G

Variant summary

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

The ENST00000716444.1(ENSG00000276407):​n.384-1263C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0875 in 152,212 control chromosomes in the GnomAD database, including 814 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 0.088 (814 hom., cov: 32)
• Consequence: ENSG00000276407 ENST00000716444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.981
• Publications: 1 publications found

Genes affected

LOC102724877 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716444.1. 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
	ENSG00000276407	ENST00000716444.1		n.384-1263C>G		intron	N/A
	ENSG00000276407	ENST00000716445.1		n.220-1263C>G		intron	N/A
	ENSG00000276407	ENST00000716446.1		n.365-1263C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0876 AC: 13319 AN: 152094 Hom.: 817 Cov.: 32

Gnomad AFR AF: 0.0375

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0792

Gnomad FIN AF: 0.0972

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0893

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0875 AC: 13320 AN: 152212 Hom.: 814 Cov.: 32 AF XY: 0.0909 AC XY: 6763 AN XY: 74406

African (AFR) AF: 0.0374 AC: 1555 AN: 41556

American (AMR) AF: 0.123 AC: 1873 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3472

East Asian (EAS) AF: 0.316 AC: 1634 AN: 5178

South Asian (SAS) AF: 0.0790 AC: 380 AN: 4808

European-Finnish (FIN) AF: 0.0972 AC: 1029 AN: 10588

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0894 AC: 6077 AN: 68006

Other (OTH) AF: 0.0870 AC: 184 AN: 2114

Alfa AF: 0.0866 Hom.: 74

Bravo AF: 0.0872

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.043
DANN	Benign	0.61
PhyloP100		-0.98

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: rs3952812;

hg19: chr3-193808033;