5-79803175-C-T

Variant names:

• chr5-79803175-C-T
• rs259067
• ENST00000421252.2:n.125+663G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000421252.2(ENSG00000250258):​n.125+663G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,134 control chromosomes in the GnomAD database, including 4,228 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 0.22 (4228 hom., cov: 33)
• Consequence: ENSG00000250258 ENST00000421252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

ENSG00000250258 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250258	ENST00000421252.2	n.125+663G>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34130 AN: 152016 Hom.: 4219 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.451

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.225 AC: 34170 AN: 152134 Hom.: 4228 Cov.: 33 AF XY: 0.231 AC XY: 17175 AN XY: 74370

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.219

Alfa AF: 0.189 Hom.: 6030

Bravo AF: 0.233

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs259067; hg19: chr5-79098998;