rs11681243

Variant names:

• chr2-48024017-G-T
• rs11681243
• ENST00000447571.5:n.241-20592C>A

Variant summary

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

The ENST00000447571.5(ENSG00000230773):​n.241-20592C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,116 control chromosomes in the GnomAD database, including 905 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 0.10 (905 hom., cov: 32)
• Consequence: ENSG00000230773 ENST00000447571.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

ENSG00000230773 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.125 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
ENSG00000230773	ENST00000447571.5	n.241-20592C>A		intron_variant	Intron 3 of 8	1
ENSG00000230773	ENST00000587616.1	n.191-1614C>A		intron_variant	Intron 2 of 10	5
ENSG00000230773	ENST00000649883.1	n.202-20592C>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15378 AN: 151998 Hom.: 904 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.0617

Gnomad AMR AF: 0.0732

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.0973

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

GnomAD4 genome AF: 0.101 AC: 15390 AN: 152116 Hom.: 905 Cov.: 32 AF XY: 0.0993 AC XY: 7382 AN XY: 74372

Gnomad4 AFR AF: 0.0859

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0166

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.0958

Alfa AF: 0.111 Hom.: 168

Bravo AF: 0.0945

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11681243; hg19: chr2-48251156;