11-96956412-C-G

Variant summary

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

The ENST00000661755.1(ENSG00000254587):n.242-19251C>G 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 0.552 in 151,314 control chromosomes in the GnomAD database, including 23,257 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 0.55 (23257 hom., cov: 33)
• Consequence: ENST00000661755.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196

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 (EAS) allele frequency at 95% confidence interval = 0.694 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
	ENST00000661755.1	n.242-19251C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83533 AN: 151202 Hom.: 23267 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.593

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.552 AC: 83540 AN: 151314 Hom.: 23257 Cov.: 33 AF XY: 0.558 AC XY: 41258 AN XY: 73934

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.570

Alfa AF: 0.409 Hom.: 1065

Bravo AF: 0.547

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs651263; hg19: chr11-96827412;