rs13073411

chr3-30440818-C-T

Variant summary

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

The ENST00000691186.1(ENSG00000289450):n.213-28215C>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 0.152 in 152,128 control chromosomes in the GnomAD database, including 1,906 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 0.15 (1906 hom., cov: 32)
• Consequence: ENST00000691186.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105377013	XR_940683.2	n.293+189G>A		intron_variant, non_coding_transcript_variant
LOC101927995	XR_001740627.2	n.213-28215C>T		intron_variant, non_coding_transcript_variant
LOC101927995	XR_001740628.2	n.261-28215C>T		intron_variant, non_coding_transcript_variant
LOC101927995	XR_007095856.1	n.257-28215C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000691186.1	n.213-28215C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23144 AN: 152010 Hom.: 1907 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.152 AC: 23147 AN: 152128 Hom.: 1906 Cov.: 32 AF XY: 0.152 AC XY: 11318 AN XY: 74360

Gnomad4 AFR AF: 0.127

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.196

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.167

Alfa AF: 0.174 Hom.: 4960

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.9
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13073411; hg19: chr3-30482310;