rs4490198

Variant names:

• chr2-114406882-G-A
• rs4490198
• ENST00000801757.1:n.223-30854G>A

Variant summary

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

The ENST00000801757.1(ENSG00000304278):​n.223-30854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,996 control chromosomes in the GnomAD database, including 22,688 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 0.54 (22688 hom., cov: 32)
• Consequence: ENSG00000304278 ENST00000801757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 6 publications found

Genes affected

ENSG00000304278 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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
ENSG00000304278	ENST00000801757.1	n.223-30854G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81838 AN: 151880 Hom.: 22687 Cov.: 32

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.644

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.645

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.539 AC: 81852 AN: 151996 Hom.: 22688 Cov.: 32 AF XY: 0.539 AC XY: 40064 AN XY: 74306

African (AFR) AF: 0.415 AC: 17208 AN: 41438

American (AMR) AF: 0.643 AC: 9823 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2535 AN: 3470

East Asian (EAS) AF: 0.647 AC: 3348 AN: 5178

South Asian (SAS) AF: 0.551 AC: 2655 AN: 4818

European-Finnish (FIN) AF: 0.479 AC: 5051 AN: 10542

Middle Eastern (MID) AF: 0.774 AC: 226 AN: 292

European-Non Finnish (NFE) AF: 0.577 AC: 39247 AN: 67964

Other (OTH) AF: 0.592 AC: 1250 AN: 2112

Alfa AF: 0.567 Hom.: 13010

Bravo AF: 0.547

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.72
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs4490198; hg19: chr2-115164459;