chr5-79807648-G-C

Variant names:

• chr5-79807648-G-C
• rs4704591
• ENST00000421252.2:n.72-3757C>G

Variant summary

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

The ENST00000421252.2(ENSG00000250258):​n.72-3757C>G variant causes a intron 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: ENSG00000250258 ENST00000421252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 14 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.376 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000250258	ENST00000421252.2	TSL:3	n.72-3757C>G		intron	N/A
	ENSG00000286818	ENST00000827626.1		n.83+5894G>C		intron	N/A

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

African (AFR) AF: 0.125 AC: 5174 AN: 41512

American (AMR) AF: 0.275 AC: 4208 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3468

East Asian (EAS) AF: 0.227 AC: 1170 AN: 5164

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4820

European-Finnish (FIN) AF: 0.336 AC: 3546 AN: 10562

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25851 AN: 67968

Other (OTH) AF: 0.298 AC: 630 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.86
DANN	Benign	0.42
PhyloP100		-0.098
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4704591; hg19: chr5-79103471;