chr5-159376078-A-G

Variant names:

• chr5-159376078-A-G
• rs6897260
• ENST00000635333.1:n.283-16455A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635333.1(ENSG00000249738):​n.283-16455A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,178 control chromosomes in the GnomAD database, including 43,736 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 0.75 (43736 hom., cov: 33)
• Consequence: ENSG00000249738 ENST00000635333.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

Genes affected

ENSG00000249738 (HGNC:58156):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 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
ENSG00000249738	ENST00000635333.1	n.283-16455A>G		intron_variant	Intron 3 of 7	5
ENSG00000249738	ENST00000641150.1	n.532+21957A>G		intron_variant	Intron 4 of 4
ENSG00000249738	ENST00000648969.1	n.53+21957A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114750 AN: 152060 Hom.: 43678 Cov.: 33

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.907

Gnomad SAS AF: 0.832

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.742

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

GnomAD4 genome AF: 0.755 AC: 114872 AN: 152178 Hom.: 43736 Cov.: 33 AF XY: 0.763 AC XY: 56740 AN XY: 74394

Gnomad4 AFR AF: 0.830

Gnomad4 AMR AF: 0.790

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.908

Gnomad4 SAS AF: 0.832

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.744

Alfa AF: 0.741 Hom.: 7263

Bravo AF: 0.758

Asia WGS AF: 0.874 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.92
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6897260; hg19: chr5-158803086;