rs13156086

chr5-111079771-A-C

Variant summary

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

The ENST00000507269.3(ENSG00000253613):n.213-2295T>G 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 0.248 in 152,104 control chromosomes in the GnomAD database, including 5,491 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 (5491 hom., cov: 32)
• Consequence: ENST00000507269.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 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
	ENST00000507269.3	n.213-2295T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37760 AN: 151986 Hom.: 5490 Cov.: 32

Gnomad AFR AF: 0.0971

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.248 AC: 37758 AN: 152104 Hom.: 5491 Cov.: 32 AF XY: 0.255 AC XY: 18921 AN XY: 74338

Gnomad4 AFR AF: 0.0968

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.379

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.267

Alfa AF: 0.244 Hom.: 719

Bravo AF: 0.234

Asia WGS AF: 0.276 AC: 961 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	8.2
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13156086; hg19: chr5-110415469;