rs2057178

Positions:

• chr11-32342641-G-A

Variant summary

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

The ENST00000525689.2(ENSG00000293378):​n.122+647C>T 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 0.18 in 151,356 control chromosomes in the GnomAD database, including 2,852 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 0.18 (2852 hom., cov: 31)
• Consequence: ENST00000525689.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000525689.2	n.122+647C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27213 AN: 151288 Hom.: 2844 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0586

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.0698

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 27228 AN: 151356 Hom.: 2852 Cov.: 31 AF XY: 0.175 AC XY: 12921 AN XY: 73818

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0581

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0698

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.173

Alfa AF: 0.159 Hom.: 2096

Bravo AF: 0.182

Asia WGS AF: 0.157 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2057178; hg19: chr11-32364187;