rs4492018

Variant names:

• chr4-122593373-G-A
• rs4492018
• ENST00000776599.1:n.557-3366C>T

Variant summary

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

The ENST00000776599.1(ENSG00000301148):​n.557-3366C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 151,988 control chromosomes in the GnomAD database, including 9,924 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 0.35 (9924 hom., cov: 32)
• Consequence: ENSG00000301148 ENST00000776599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 9 publications found

Genes affected

ENSG00000301148 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.492 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
ENSG00000301148	ENST00000776599.1	n.557-3366C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53032 AN: 151866 Hom.: 9899 Cov.: 32

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.349 AC: 53096 AN: 151988 Hom.: 9924 Cov.: 32 AF XY: 0.353 AC XY: 26267 AN XY: 74308

African (AFR) AF: 0.460 AC: 19041 AN: 41434

American (AMR) AF: 0.386 AC: 5899 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1202 AN: 3462

East Asian (EAS) AF: 0.426 AC: 2198 AN: 5158

South Asian (SAS) AF: 0.509 AC: 2454 AN: 4820

European-Finnish (FIN) AF: 0.255 AC: 2700 AN: 10568

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18325 AN: 67952

Other (OTH) AF: 0.371 AC: 785 AN: 2114

Alfa AF: 0.316 Hom.: 5035

Bravo AF: 0.362

Asia WGS AF: 0.487 AC: 1696 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.25
DANN	Benign	0.83
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs4492018; hg19: chr4-123514528;