rs747559

Variant names:

• chr4-102493018-A-G
• rs747559
• ENST00000843825.1:n.49+9421T>C

Variant summary

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

The ENST00000843825.1(ENSG00000248161):​n.49+9421T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 151,816 control chromosomes in the GnomAD database, including 14,292 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 0.43 (14292 hom., cov: 30)
• Consequence: ENSG00000248161 ENST00000843825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.255
• Publications: 16 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.49 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1	n.48+9421T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000843825.1	n.49+9421T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65141 AN: 151698 Hom.: 14264 Cov.: 30

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.430 AC: 65213 AN: 151816 Hom.: 14292 Cov.: 30 AF XY: 0.430 AC XY: 31927 AN XY: 74194

African (AFR) AF: 0.495 AC: 20492 AN: 41358

American (AMR) AF: 0.487 AC: 7432 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1157 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2101 AN: 5164

South Asian (SAS) AF: 0.296 AC: 1426 AN: 4810

European-Finnish (FIN) AF: 0.449 AC: 4732 AN: 10534

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26610 AN: 67902

Other (OTH) AF: 0.400 AC: 844 AN: 2112

Alfa AF: 0.434 Hom.: 3173

Bravo AF: 0.440

Asia WGS AF: 0.355 AC: 1231 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.35
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs747559; hg19: chr4-103414175; COSMIC: COSV60118891;