4-166283823-G-C

Variant names:

• chr4-166283823-G-C
• rs433130
• ENST00000835335.1:n.295-36171G>C

Variant summary

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

The ENST00000835335.1(ENSG00000308604):​n.295-36171G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,116 control chromosomes in the GnomAD database, including 55,671 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 0.84 (55671 hom., cov: 32)
• Consequence: ENSG00000308604 ENST00000835335.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 2 publications found

Genes affected

ENSG00000308604 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308604	ENST00000835335.1	n.295-36171G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128106 AN: 151998 Hom.: 55655 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.968

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.843 AC: 128179 AN: 152116 Hom.: 55671 Cov.: 32 AF XY: 0.836 AC XY: 62144 AN XY: 74352

African (AFR) AF: 0.710 AC: 29441 AN: 41486

American (AMR) AF: 0.821 AC: 12537 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3310 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1525 AN: 5154

South Asian (SAS) AF: 0.812 AC: 3919 AN: 4828

European-Finnish (FIN) AF: 0.921 AC: 9773 AN: 10606

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64695 AN: 68000

Other (OTH) AF: 0.866 AC: 1823 AN: 2104

Alfa AF: 0.893 Hom.: 3084

Bravo AF: 0.825

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.73
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs433130; hg19: chr4-167204975;