rs4704591

Positions:

• chr5-79807648-G-C

Variant summary

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

The ENST00000421252.2(ENSG00000250258):​n.72-3757C>G 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 0.287 in 152,096 control chromosomes in the GnomAD database, including 7,258 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 0.29 (7258 hom., cov: 32)
• Consequence: ENST00000421252.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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.72-3757C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43695 AN: 151978 Hom.: 7256 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.287 AC: 43686 AN: 152096 Hom.: 7258 Cov.: 32 AF XY: 0.285 AC XY: 21165 AN XY: 74318

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.227

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.380

Gnomad4 OTH AF: 0.298

Alfa AF: 0.337 Hom.: 1140

Bravo AF: 0.274

Asia WGS AF: 0.217 AC: 753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.86
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4704591; hg19: chr5-79103471;