5-25967594-T-C

Variant names:

• chr5-25967594-T-C
• rs4307059
• ENST00000658114.2:n.124+3644T>C

Variant summary

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

The ENST00000658114.2(ENSG00000286625):​n.124+3644T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,054 control chromosomes in the GnomAD database, including 7,337 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 0.28 (7337 hom., cov: 32)
• Consequence: ENSG00000286625 ENST00000658114.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195
• Publications: 79 publications found

Genes affected

ENSG00000286625 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.372 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658114.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286625	ENST00000658114.2		n.124+3644T>C		intron	N/A
	ENSG00000286625	ENST00000668718.1		n.49+3644T>C		intron	N/A
	ENSG00000286625	ENST00000759668.1		n.115+3644T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41878 AN: 151936 Hom.: 7336 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.275 AC: 41884 AN: 152054 Hom.: 7337 Cov.: 32 AF XY: 0.278 AC XY: 20639 AN XY: 74324

African (AFR) AF: 0.0696 AC: 2892 AN: 41528

American (AMR) AF: 0.268 AC: 4086 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3472

East Asian (EAS) AF: 0.152 AC: 785 AN: 5162

South Asian (SAS) AF: 0.311 AC: 1499 AN: 4818

European-Finnish (FIN) AF: 0.419 AC: 4424 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25531 AN: 67944

Other (OTH) AF: 0.300 AC: 634 AN: 2110

Alfa AF: 0.341 Hom.: 31736

Bravo AF: 0.256

Asia WGS AF: 0.240 AC: 835 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		0.20

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4307059;

hg19: chr5-25967703;