chr11-43857990-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

ENSG00000246250 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000530450.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000246250	ENST00000530450.1	TSL:4	n.248-9474T>C		intron	N/A
	ENSG00000246250	ENST00000720674.1		n.133-10663T>C		intron	N/A

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

African (AFR) AF: 0.185 AC: 7681 AN: 41496

American (AMR) AF: 0.426 AC: 6514 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1309 AN: 3464

East Asian (EAS) AF: 0.175 AC: 905 AN: 5174

South Asian (SAS) AF: 0.185 AC: 890 AN: 4816

European-Finnish (FIN) AF: 0.470 AC: 4955 AN: 10544

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24329 AN: 67970

Other (OTH) AF: 0.317 AC: 667 AN: 2104

Alfa AF: 0.343 Hom.: 17723

Bravo AF: 0.309

Asia WGS AF: 0.214 AC: 745 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	10
DANN	Benign	0.83
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs11037685; hg19: chr11-43879540;