5-73136209-C-G

Variant names:

• chr5-73136209-C-G
• rs17663555
• ENST00000508255.1:n.174-3926G>C

Variant summary

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

The ENST00000508255.1(ENSG00000251599):​n.174-3926G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 152,162 control chromosomes in the GnomAD database, including 5,542 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 0.26 (5542 hom., cov: 33)
• Consequence: ENSG00000251599 ENST00000508255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.656
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.339 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379030	NR_134252.1		n.174-3926G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251599	ENST00000508255.1	TSL:3	n.174-3926G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39722 AN: 152044 Hom.: 5543 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.261 AC: 39724 AN: 152162 Hom.: 5542 Cov.: 33 AF XY: 0.261 AC XY: 19412 AN XY: 74364

African (AFR) AF: 0.164 AC: 6808 AN: 41532

American (AMR) AF: 0.235 AC: 3589 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.352 AC: 1818 AN: 5164

South Asian (SAS) AF: 0.314 AC: 1510 AN: 4804

European-Finnish (FIN) AF: 0.285 AC: 3024 AN: 10594

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21008 AN: 67982

Other (OTH) AF: 0.269 AC: 566 AN: 2108

Alfa AF: 0.280 Hom.: 3414

Bravo AF: 0.251

Asia WGS AF: 0.302 AC: 1052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.57
DANN	Benign	0.53
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs17663555; hg19: chr5-72432036;