rs11715829

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000243620 (HGNC:58947):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000473299.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243620	ENST00000473299.1	TSL:4	n.133-82818A>G		intron	N/A
	ENSG00000243620	ENST00000670466.1		n.181-82818A>G		intron	N/A

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

African (AFR) AF: 0.0109 AC: 453 AN: 41542

American (AMR) AF: 0.0353 AC: 539 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0488 AC: 169 AN: 3466

East Asian (EAS) AF: 0.00 AC: 0 AN: 5154

South Asian (SAS) AF: 0.0126 AC: 61 AN: 4828

European-Finnish (FIN) AF: 0.0457 AC: 484 AN: 10600

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0702 AC: 4768 AN: 67924

Other (OTH) AF: 0.0512 AC: 108 AN: 2108

Alfa AF: 0.0633 Hom.: 569

Bravo AF: 0.0426

Asia WGS AF: 0.00609 AC: 21 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	14
DANN	Benign	0.79
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11715829;

hg19: chr3-146957166;