rs37011

chr5-1348683-A-T

Variant summary

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

The ENST00000656081.1(ENSG00000286388):n.2257-1058A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,090 control chromosomes in the GnomAD database, including 13,988 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 0.42 (13988 hom., cov: 33)
• Consequence: ENST00000656081.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000656081.1	n.2257-1058A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64072 AN: 151972 Hom.: 13981 Cov.: 33

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.422 AC: 64117 AN: 152090 Hom.: 13988 Cov.: 33 AF XY: 0.414 AC XY: 30792 AN XY: 74338

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.413

Alfa AF: 0.427 Hom.: 1725

Bravo AF: 0.419

Asia WGS AF: 0.222 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs37011; hg19: chr5-1348798;