rs4674039

Variant names:

• chr2-215929301-C-T
• rs4674039
• ENST00000767893.1:n.238+6398C>T

Variant summary

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

The ENST00000767893.1(ENSG00000300001):​n.238+6398C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 151,802 control chromosomes in the GnomAD database, including 8,579 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 0.32 (8579 hom., cov: 31)
• Consequence: ENSG00000300001 ENST00000767893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.610
• Publications: 2 publications found

Genes affected

ENSG00000300001 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 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
ENSG00000300001	ENST00000767893.1	n.238+6398C>T		intron_variant	Intron 1 of 1
ENSG00000300001	ENST00000767894.1	n.227-2297C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48361 AN: 151680 Hom.: 8549 Cov.: 31

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.384

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.319 AC: 48439 AN: 151802 Hom.: 8579 Cov.: 31 AF XY: 0.325 AC XY: 24121 AN XY: 74154

African (AFR) AF: 0.365 AC: 15101 AN: 41344

American (AMR) AF: 0.384 AC: 5860 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 970 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3746 AN: 5152

South Asian (SAS) AF: 0.389 AC: 1869 AN: 4810

European-Finnish (FIN) AF: 0.268 AC: 2820 AN: 10522

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.253 AC: 17160 AN: 67944

Other (OTH) AF: 0.341 AC: 718 AN: 2108

Alfa AF: 0.283 Hom.: 27975

Bravo AF: 0.338

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.27
DANN	Benign	0.40
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs4674039; hg19: chr2-216794024;