5-1349420-A-G

Variant names:

• chr5-1349420-A-G
• rs37010
• ENST00000656081.1:n.2257-321A>G

Variant summary

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

The ENST00000656081.1(ENSG00000286388):​n.2257-321A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 151,808 control chromosomes in the GnomAD database, including 15,894 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 0.45 (15894 hom., cov: 31)
• Consequence: ENSG00000286388 ENST00000656081.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

ENSG00000286388 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.566 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
ENSG00000286388	ENST00000656081.1	n.2257-321A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67580 AN: 151690 Hom.: 15878 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.422

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.446 AC: 67642 AN: 151808 Hom.: 15894 Cov.: 31 AF XY: 0.437 AC XY: 32418 AN XY: 74154

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.422

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.426

Alfa AF: 0.308 Hom.: 759

Bravo AF: 0.447

Asia WGS AF: 0.230 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37010; hg19: chr5-1349535;