5-79803175-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

ENSG00000250258 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000421252.2. 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
	ENSG00000250258	ENST00000421252.2	TSL:3	n.125+663G>A		intron	N/A
	ENSG00000286818	ENST00000827626.1		n.83+1421C>T		intron	N/A

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

African (AFR) AF: 0.235 AC: 9771 AN: 41498

American (AMR) AF: 0.313 AC: 4788 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 718 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2333 AN: 5172

South Asian (SAS) AF: 0.206 AC: 994 AN: 4822

European-Finnish (FIN) AF: 0.272 AC: 2874 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11915 AN: 67986

Other (OTH) AF: 0.219 AC: 462 AN: 2114

Alfa AF: 0.194 Hom.: 13778

Bravo AF: 0.233

Asia WGS AF: 0.311 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs259067; hg19: chr5-79098998;