rs2852438

chr11-114343980-A-G

Variant summary

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

The ENST00000544925.1(ENSG00000256947):n.50+12542T>C 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 0.096 in 151,846 control chromosomes in the GnomAD database, including 749 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 0.096 (749 hom., cov: 31)
• Consequence: ENST00000544925.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.121 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
	ENST00000544925.1	n.50+12542T>C		intron_variant, non_coding_transcript_variant		5
	ENST00000658199.1	n.492-616T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14563 AN: 151728 Hom.: 752 Cov.: 31

Gnomad AFR AF: 0.124

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000772

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0799

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0940

Gnomad OTH AF: 0.0905

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

GnomAD4 genome AF: 0.0960 AC: 14570 AN: 151846 Hom.: 749 Cov.: 31 AF XY: 0.0934 AC XY: 6930 AN XY: 74186

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.0779

Gnomad4 FIN AF: 0.0799

Gnomad4 NFE AF: 0.0940

Gnomad4 OTH AF: 0.0905

Alfa AF: 0.0965 Hom.: 1021

Bravo AF: 0.0963

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.35
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2852438; hg19: chr11-114214702;