rs11944443

Variant names:

• chr4-102499861-A-G
• rs11944443
• ENST00000843825.1:n.49+2578T>C

Your query was ambiguous. Multiple possible variants found:

• chr4-102499861-A-G
• chr4-102499861-A-T

Variant summary

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

The ENST00000843825.1(ENSG00000248161):​n.49+2578T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 151,960 control chromosomes in the GnomAD database, including 2,367 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 0.13 (2367 hom., cov: 31)
• Consequence: ENSG00000248161 ENST00000843825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.340
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1	n.48+2578T>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+2578T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18971 AN: 151842 Hom.: 2360 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.0703

Gnomad AMR AF: 0.0625

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.0520

Gnomad SAS AF: 0.0409

Gnomad FIN AF: 0.0654

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0469

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.125 AC: 19002 AN: 151960 Hom.: 2367 Cov.: 31 AF XY: 0.123 AC XY: 9105 AN XY: 74268

African (AFR) AF: 0.322 AC: 13347 AN: 41390

American (AMR) AF: 0.0624 AC: 952 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0176 AC: 61 AN: 3472

East Asian (EAS) AF: 0.0516 AC: 266 AN: 5160

South Asian (SAS) AF: 0.0416 AC: 200 AN: 4808

European-Finnish (FIN) AF: 0.0654 AC: 692 AN: 10578

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0469 AC: 3191 AN: 67980

Other (OTH) AF: 0.101 AC: 212 AN: 2104

Alfa AF: 0.0241 Hom.: 13

Bravo AF: 0.135

Asia WGS AF: 0.0660 AC: 229 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	4.6
DANN	Benign	0.77
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs11944443; hg19: chr4-103421018;