5-159302939-C-T

Variant names:

• chr5-159302939-C-T
• rs7730126
• ENST00000765301.1:n.222-247G>A

Variant summary

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

The ENST00000765301.1(ENSG00000299638):​n.222-247G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,952 control chromosomes in the GnomAD database, including 5,405 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 (5405 hom., cov: 32)
• Consequence: ENSG00000299638 ENST00000765301.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.780
• Publications: 11 publications found

Genes affected

ENSG00000299638 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299638	ENST00000765301.1	n.222-247G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39934 AN: 151834 Hom.: 5395 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.263 AC: 39969 AN: 151952 Hom.: 5405 Cov.: 32 AF XY: 0.262 AC XY: 19438 AN XY: 74236

African (AFR) AF: 0.205 AC: 8497 AN: 41428

American (AMR) AF: 0.257 AC: 3919 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1368 AN: 3466

East Asian (EAS) AF: 0.218 AC: 1124 AN: 5166

South Asian (SAS) AF: 0.184 AC: 886 AN: 4822

European-Finnish (FIN) AF: 0.319 AC: 3356 AN: 10536

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19900 AN: 67944

Other (OTH) AF: 0.295 AC: 623 AN: 2110

Alfa AF: 0.289 Hom.: 8211

Bravo AF: 0.261

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs7730126; hg19: chr5-158729947;