5-79803175-C-T

Position:

• chr5-79803175-C-T

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, non coding transcript 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: ENST00000421252.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000421252.2	n.125+663G>A		intron_variant, non_coding_transcript_variant		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;