rs11681243

chr2-48024017-G-T

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, non coding transcript 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: ENST00000447571.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651429.1	n.216-20592C>A		intron_variant, non_coding_transcript_variant

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;