5-4720472-G-C

Variant names:

• chr5-4720472-G-C
• rs7727102
• ENST00000507435.1:n.429+64399C>G

Variant summary

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

The ENST00000651524.1(ENSG00000248973):​n.212-13103C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,930 control chromosomes in the GnomAD database, including 9,295 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 0.31 (9295 hom., cov: 32)
• Consequence: ENSG00000248973 ENST00000651524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.524
• Publications: 5 publications found

Genes affected

ENSG00000248973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651524.1. 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
	ENSG00000248973	ENST00000507435.1	TSL:5	n.429+64399C>G		intron	N/A
	ENSG00000248973	ENST00000651524.1		n.212-13103C>G		intron	N/A
	ENSG00000248973	ENST00000847489.1		n.349-82743C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47678 AN: 151814 Hom.: 9271 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.314 AC: 47764 AN: 151930 Hom.: 9295 Cov.: 32 AF XY: 0.313 AC XY: 23255 AN XY: 74262

African (AFR) AF: 0.558 AC: 23125 AN: 41412

American (AMR) AF: 0.334 AC: 5092 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 498 AN: 3466

East Asian (EAS) AF: 0.228 AC: 1175 AN: 5150

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4810

European-Finnish (FIN) AF: 0.217 AC: 2288 AN: 10564

Middle Eastern (MID) AF: 0.253 AC: 74 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13640 AN: 67964

Other (OTH) AF: 0.257 AC: 542 AN: 2110

Alfa AF: 0.263 Hom.: 816

Bravo AF: 0.337

Asia WGS AF: 0.262 AC: 910 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.56
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs7727102; hg19: chr5-4720585;