rs243908

Variant names:

• chr11-112135216-A-G
• rs243908
• ENST00000532699.1:n.315-35203A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-112135216-A-G
• chr11-112135216-A-T

Variant summary

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

The ENST00000532699.1(ENSG00000255292):​n.315-35203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,998 control chromosomes in the GnomAD database, including 6,138 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 0.28 (6138 hom., cov: 30)
• Consequence: ENSG00000255292 ENST00000532699.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.67

Genes affected

ENSG00000255292 (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 (AMR) allele frequency at 95% confidence interval = 0.319 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
ENSG00000255292	ENST00000532699.1	n.315-35203A>G		intron_variant	Intron 3 of 5	3		ENSP00000456434.1
ENSG00000255292	ENST00000525987.5	n.320-35203A>G		intron_variant	Intron 3 of 5	4
ENSG00000255292	ENST00000531744.5	n.315-35203A>G		intron_variant	Intron 3 of 5	2		ENSP00000456957.1

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42352 AN: 151880 Hom.: 6140 Cov.: 30

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.279 AC: 42341 AN: 151998 Hom.: 6138 Cov.: 30 AF XY: 0.279 AC XY: 20703 AN XY: 74288

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.323

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.271

Alfa AF: 0.293 Hom.: 9124

Bravo AF: 0.278

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.0
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs243908; hg19: chr11-112005939;