11-43870144-C-T

Variant names:

• chr11-43870144-C-T
• rs2862999
• ENST00000530450.1:n.247+7839G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000530450.1(ENSG00000246250):​n.247+7839G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.714 in 152,132 control chromosomes in the GnomAD database, including 41,841 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 0.71 (41841 hom., cov: 32)
• Consequence: ENSG00000246250 ENST00000530450.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.874
• Publications: 5 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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.247+7839G>A		intron_variant	Intron 2 of 3	4
ENSG00000246250	ENST00000720674.1	n.132+7839G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.714 AC: 108610 AN: 152014 Hom.: 41824 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.886

Gnomad FIN AF: 0.850

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.731

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

GnomAD4 genome AF: 0.714 AC: 108682 AN: 152132 Hom.: 41841 Cov.: 32 AF XY: 0.721 AC XY: 53668 AN XY: 74406

African (AFR) AF: 0.401 AC: 16603 AN: 41444

American (AMR) AF: 0.777 AC: 11880 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2957 AN: 3472

East Asian (EAS) AF: 0.918 AC: 4759 AN: 5186

South Asian (SAS) AF: 0.886 AC: 4280 AN: 4828

European-Finnish (FIN) AF: 0.850 AC: 9000 AN: 10594

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.834 AC: 56719 AN: 68010

Other (OTH) AF: 0.734 AC: 1551 AN: 2112

Alfa AF: 0.789 Hom.: 147313

Bravo AF: 0.693

Asia WGS AF: 0.881 AC: 3059 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.72
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2862999; hg19: chr11-43891694;