rs11037685

Variant names:

• chr11-43857990-A-G
• rs11037685
• ENST00000530450.1:n.248-9474T>C

Variant summary

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

The ENST00000530450.1(ENSG00000246250):​n.248-9474T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,048 control chromosomes in the GnomAD database, including 8,180 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 0.31 (8180 hom., cov: 32)
• Consequence: ENSG00000246250 ENST00000530450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463

Genes affected

ENSG00000246250 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.418 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
ENSG00000246250	ENST00000530450.1	n.248-9474T>C		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47606 AN: 151930 Hom.: 8177 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.313 AC: 47623 AN: 152048 Hom.: 8180 Cov.: 32 AF XY: 0.314 AC XY: 23348 AN XY: 74320

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.317

Alfa AF: 0.347 Hom.: 13153

Bravo AF: 0.309

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11037685; hg19: chr11-43879540;