rs230490

Variant names:

• chr4-102466262-G-A
• rs230490
• ENST00000843825.1:n.50-16195C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-102466262-G-A
• chr4-102466262-G-C
• chr4-102466262-G-T

Variant summary

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

The ENST00000843825.1(ENSG00000248161):​n.50-16195C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 151,920 control chromosomes in the GnomAD database, including 10,390 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 (10390 hom., cov: 31)
• Consequence: ENSG00000248161 ENST00000843825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 7 publications found

Genes affected

ENSG00000248161 (HGNC:58149):

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 (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1	n.49-16195C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000843825.1	n.50-16195C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52749 AN: 151802 Hom.: 10397 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.345

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.347 AC: 52743 AN: 151920 Hom.: 10390 Cov.: 31 AF XY: 0.350 AC XY: 26014 AN XY: 74236

African (AFR) AF: 0.160 AC: 6638 AN: 41434

American (AMR) AF: 0.450 AC: 6867 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.345 AC: 1194 AN: 3464

East Asian (EAS) AF: 0.587 AC: 3041 AN: 5180

South Asian (SAS) AF: 0.380 AC: 1833 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4240 AN: 10536

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.408 AC: 27720 AN: 67930

Other (OTH) AF: 0.356 AC: 752 AN: 2110

Alfa AF: 0.388 Hom.: 17296

Bravo AF: 0.343

Asia WGS AF: 0.471 AC: 1638 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	1.7
DANN	Benign	0.42
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs230490; hg19: chr4-103387419;