rs6533015

Variant names:

• chr4-102434376-C-G
• rs6533015
• ENST00000512915.5:n.81-14582G>C

Your query was ambiguous. Multiple possible variants found:

• chr4-102434376-C-G
• chr4-102434376-C-T

Variant summary

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

The ENST00000512915.5(ENSG00000248161):​n.81-14582G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 151,866 control chromosomes in the GnomAD database, including 31,105 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 0.63 (31105 hom., cov: 31)
• Consequence: ENSG00000248161 ENST00000512915.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 5 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=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1	n.186-14582G>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000512915.5	n.81-14582G>C		intron_variant	Intron 1 of 3	5
ENSG00000248161	ENST00000843825.1	n.187-15388G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95674 AN: 151748 Hom.: 31051 Cov.: 31

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.631 AC: 95787 AN: 151866 Hom.: 31105 Cov.: 31 AF XY: 0.628 AC XY: 46638 AN XY: 74208

African (AFR) AF: 0.779 AC: 32298 AN: 41438

American (AMR) AF: 0.531 AC: 8105 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1890 AN: 5158

South Asian (SAS) AF: 0.631 AC: 3036 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6166 AN: 10520

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39941 AN: 67898

Other (OTH) AF: 0.628 AC: 1320 AN: 2102

Alfa AF: 0.606 Hom.: 3376

Bravo AF: 0.632

Asia WGS AF: 0.496 AC: 1724 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.24
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs6533015; hg19: chr4-103355533;