5-5604439-T-C

Variant names:

• chr5-5604439-T-C
• rs1438675
• ENST00000796378.1:n.197-9365A>G

Variant summary

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

The ENST00000796378.1(ENSG00000303660):​n.197-9365A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,130 control chromosomes in the GnomAD database, including 5,865 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 0.25 (5865 hom., cov: 33)
• Consequence: ENSG00000303660 ENST00000796378.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.245
• Publications: 1 publications found

Genes affected

ENSG00000303660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 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
ENSG00000303660	ENST00000796378.1	n.197-9365A>G		intron_variant	Intron 2 of 4
ENSG00000303674	ENST00000796428.1	n.330-1224T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38481 AN: 152012 Hom.: 5869 Cov.: 33

Gnomad AFR AF: 0.0895

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.253 AC: 38493 AN: 152130 Hom.: 5865 Cov.: 33 AF XY: 0.260 AC XY: 19366 AN XY: 74370

African (AFR) AF: 0.0894 AC: 3713 AN: 41536

American (AMR) AF: 0.343 AC: 5246 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3470

East Asian (EAS) AF: 0.550 AC: 2843 AN: 5166

South Asian (SAS) AF: 0.410 AC: 1975 AN: 4822

European-Finnish (FIN) AF: 0.293 AC: 3091 AN: 10562

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 20015 AN: 67984

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

Alfa AF: 0.292 Hom.: 5464

Bravo AF: 0.249

Asia WGS AF: 0.443 AC: 1541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.87
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1438675; hg19: chr5-5604552;