4-102444375-G-T

Variant names:

• chr4-102444375-G-T
• rs13115343
• ENST00000512915.5:n.80+5556C>A

Variant summary

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

The ENST00000512915.5(ENSG00000248161):​n.80+5556C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,952 control chromosomes in the GnomAD database, including 11,814 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 0.36 (11814 hom., cov: 32)
• Consequence: ENSG00000248161 ENST00000512915.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.571 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512915.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NFKB1-AS1	NR_136202.1		n.185+5556C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248161	ENST00000512915.5	TSL:5	n.80+5556C>A		intron	N/A
	ENSG00000248161	ENST00000843825.1		n.186+5556C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55096 AN: 151834 Hom.: 11800 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.249

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.349

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

GnomAD4 genome AF: 0.363 AC: 55158 AN: 151952 Hom.: 11814 Cov.: 32 AF XY: 0.359 AC XY: 26662 AN XY: 74290

African (AFR) AF: 0.577 AC: 23921 AN: 41424

American (AMR) AF: 0.249 AC: 3800 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 1350 AN: 3466

East Asian (EAS) AF: 0.0324 AC: 168 AN: 5182

South Asian (SAS) AF: 0.128 AC: 619 AN: 4824

European-Finnish (FIN) AF: 0.362 AC: 3811 AN: 10532

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.301 AC: 20482 AN: 67938

Other (OTH) AF: 0.345 AC: 729 AN: 2110

Alfa AF: 0.319 Hom.: 31620

Bravo AF: 0.370

Asia WGS AF: 0.110 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.64
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs13115343; hg19: chr4-103365532;