4-25566296-C-T

Variant names:

• chr4-25566296-C-T
• rs16877243
• ENST00000671933.1:n.342+26808C>T

Variant summary

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

The NR_134641.1(LOC101929161):​n.247+2804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 151,950 control chromosomes in the GnomAD database, including 19,166 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 (19166 hom., cov: 32)
• Consequence: LOC101929161 NR_134641.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 4 publications found

Genes affected

ENSG00000248545 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_134641.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929161	NR_134641.1		n.247+2804G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248545	ENST00000671933.1		n.342+26808C>T		intron	N/A
	ENSG00000306142	ENST00000815613.1		n.263+2804G>A		intron	N/A
	ENSG00000306142	ENST00000815614.1		n.259+2804G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64364 AN: 151832 Hom.: 19122 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.424 AC: 64464 AN: 151950 Hom.: 19166 Cov.: 32 AF XY: 0.431 AC XY: 31969 AN XY: 74260

African (AFR) AF: 0.830 AC: 34434 AN: 41492

American (AMR) AF: 0.392 AC: 5970 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 973 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3213 AN: 5164

South Asian (SAS) AF: 0.474 AC: 2285 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3145 AN: 10562

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13362 AN: 67892

Other (OTH) AF: 0.389 AC: 821 AN: 2112

Alfa AF: 0.275 Hom.: 4029

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.26
DANN	Benign	0.49
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16877243; hg19: chr4-25567918;