5-75332189-G-C

Variant names:

• chr5-75332189-G-C
• rs3931914
• ENST00000501886.2:n.198+2758C>G

Variant summary

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

The ENST00000501886.2(ENSG00000247372):​n.198+2758C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,100 control chromosomes in the GnomAD database, including 4,082 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 0.23 (4082 hom., cov: 32)
• Consequence: ENSG00000247372 ENST00000501886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 8 publications found

Genes affected

ENSG00000247372 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000501886.2. 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
	ENSG00000247372	ENST00000501886.2	TSL:4	n.198+2758C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34761 AN: 151982 Hom.: 4075 Cov.: 32

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.229 AC: 34781 AN: 152100 Hom.: 4082 Cov.: 32 AF XY: 0.233 AC XY: 17340 AN XY: 74334

African (AFR) AF: 0.206 AC: 8559 AN: 41448

American (AMR) AF: 0.188 AC: 2870 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 949 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5174

South Asian (SAS) AF: 0.425 AC: 2053 AN: 4830

European-Finnish (FIN) AF: 0.244 AC: 2578 AN: 10556

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15395 AN: 68006

Other (OTH) AF: 0.234 AC: 494 AN: 2110

Alfa AF: 0.130 Hom.: 238

Bravo AF: 0.218

Asia WGS AF: 0.340 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.23
DANN	Benign	0.47
PhyloP100		-0.99

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3931914;

hg19: chr5-74628014;