4-102497800-T-C

Variant names:

• chr4-102497800-T-C
• rs980455
• ENST00000843825.1:n.49+4639A>G

Variant summary

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

The ENST00000843825.1(ENSG00000248161):​n.49+4639A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,976 control chromosomes in the GnomAD database, including 13,827 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 0.42 (13827 hom., cov: 31)
• Consequence: ENSG00000248161 ENST00000843825.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.676
• Publications: 19 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NFKB1-AS1	NR_136202.1	n.48+4639A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248161	ENST00000843825.1	n.49+4639A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64147 AN: 151858 Hom.: 13803 Cov.: 31

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.423 AC: 64213 AN: 151976 Hom.: 13827 Cov.: 31 AF XY: 0.423 AC XY: 31424 AN XY: 74278

African (AFR) AF: 0.474 AC: 19657 AN: 41442

American (AMR) AF: 0.483 AC: 7374 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3468

East Asian (EAS) AF: 0.406 AC: 2094 AN: 5158

South Asian (SAS) AF: 0.287 AC: 1381 AN: 4806

European-Finnish (FIN) AF: 0.449 AC: 4745 AN: 10558

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26554 AN: 67958

Other (OTH) AF: 0.394 AC: 834 AN: 2116

Alfa AF: 0.410 Hom.: 2164

Bravo AF: 0.432

Asia WGS AF: 0.351 AC: 1219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs980455; hg19: chr4-103418957;