rs11715829

Variant names:

• chr3-147239379-T-C
• rs11715829
• ENST00000473299.1:n.133-82818A>G

Variant summary

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

The ENST00000473299.1(ENSG00000243620):​n.133-82818A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,116 control chromosomes in the GnomAD database, including 227 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 0.044 (227 hom., cov: 32)
• Consequence: ENSG00000243620 ENST00000473299.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.978

Genes affected

ENSG00000243620 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0685 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
ENSG00000243620	ENST00000473299.1	n.133-82818A>G		intron_variant	Intron 2 of 5	4
ENSG00000243620	ENST00000670466.1	n.181-82818A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6736 AN: 151998 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0109

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0353

Gnomad ASJ AF: 0.0488

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0702

Gnomad OTH AF: 0.0518

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

GnomAD4 genome AF: 0.0442 AC: 6731 AN: 152116 Hom.: 227 Cov.: 32 AF XY: 0.0419 AC XY: 3113 AN XY: 74374

Gnomad4 AFR AF: 0.0109

Gnomad4 AMR AF: 0.0353

Gnomad4 ASJ AF: 0.0488

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0702

Gnomad4 OTH AF: 0.0512

Alfa AF: 0.0653 Hom.: 481

Bravo AF: 0.0426

Asia WGS AF: 0.00609 AC: 21 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11715829; hg19: chr3-146957166;