ENST00000420000.6:n.201-35226G>C

Variant names:

• chr3-3417876-C-G
• rs4685635
• ENST00000420000.6:n.201-35226G>C

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.201-35226G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.638 in 151,770 control chromosomes in the GnomAD database, including 31,300 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 0.64 (31300 hom., cov: 31)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 2 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.669 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
ENSG00000223727	ENST00000420000.6	n.201-35226G>C		intron_variant	Intron 2 of 4	4
ENSG00000223727	ENST00000451031.5	n.175+23032G>C		intron_variant	Intron 2 of 5	3
ENSG00000223727	ENST00000455703.1	n.60-35226G>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.638 AC: 96716 AN: 151648 Hom.: 31273 Cov.: 31

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.756

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.649

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

GnomAD4 genome AF: 0.638 AC: 96790 AN: 151770 Hom.: 31300 Cov.: 31 AF XY: 0.641 AC XY: 47524 AN XY: 74172

African (AFR) AF: 0.552 AC: 22848 AN: 41356

American (AMR) AF: 0.667 AC: 10175 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2260 AN: 3468

East Asian (EAS) AF: 0.457 AC: 2360 AN: 5160

South Asian (SAS) AF: 0.681 AC: 3276 AN: 4810

European-Finnish (FIN) AF: 0.751 AC: 7893 AN: 10510

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.674 AC: 45757 AN: 67914

Other (OTH) AF: 0.647 AC: 1360 AN: 2102

Alfa AF: 0.502 Hom.: 1158

Bravo AF: 0.628

Asia WGS AF: 0.583 AC: 2020 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.091
DANN	Benign	0.32
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4685635; hg19: chr3-3459560;