chr5-73135655-G-C

Variant names:

• chr5-73135655-G-C
• rs17632159
• ENST00000508255.1:n.174-3372C>G

Variant summary

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

The ENST00000508255.1(ENSG00000251599):​n.174-3372C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,166 control chromosomes in the GnomAD database, including 5,708 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 0.27 (5708 hom., cov: 33)
• Consequence: ENSG00000251599 ENST00000508255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 33 publications found

Genes affected

ENSG00000251599 (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 (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000508255.1. 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
	LOC105379030	NR_134252.1		n.174-3372C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251599	ENST00000508255.1	TSL:3	n.174-3372C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40721 AN: 152048 Hom.: 5708 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.268 AC: 40736 AN: 152166 Hom.: 5708 Cov.: 33 AF XY: 0.267 AC XY: 19863 AN XY: 74400

African (AFR) AF: 0.187 AC: 7782 AN: 41520

American (AMR) AF: 0.292 AC: 4467 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3472

East Asian (EAS) AF: 0.276 AC: 1424 AN: 5166

South Asian (SAS) AF: 0.361 AC: 1740 AN: 4820

European-Finnish (FIN) AF: 0.241 AC: 2551 AN: 10602

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.305 AC: 20766 AN: 67986

Other (OTH) AF: 0.279 AC: 589 AN: 2110

Alfa AF: 0.155 Hom.: 298

Bravo AF: 0.269

Asia WGS AF: 0.309 AC: 1072 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	1.7
DANN	Benign	0.38
PhyloP100		0.12

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: rs17632159;

hg19: chr5-72431482;