chr3-194090244-C-G

Variant names:

• chr3-194090244-C-G
• rs3952812
• ENST00000716444.1:n.384-1263C>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

ENSG00000276407 (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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724877	XM_011513352.4	c.280-1263C>G		intron_variant	Intron 3 of 5		XP_011511654.1
LOC102724877	XM_011513353.4	c.229-1263C>G		intron_variant	Intron 3 of 5		XP_011511655.1
LOC102724877	XM_011513355.4	c.393-1263C>G		intron_variant	Intron 4 of 4		XP_011511657.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000276407	ENST00000716444.1	n.384-1263C>G		intron_variant	Intron 4 of 7
ENSG00000276407	ENST00000716445.1	n.220-1263C>G		intron_variant	Intron 3 of 6
ENSG00000276407	ENST00000716446.1	n.365-1263C>G		intron_variant	Intron 4 of 8

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 v4.3

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

Other links and lift over

dbSNP: rs3952812; hg19: chr3-193808033;