11-95648004-C-T

Position:

• chr11-95648004-C-T

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+75796C>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 0.152 in 152,058 control chromosomes in the GnomAD database, including 1,778 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 0.15 (1778 hom., cov: 32)
• Consequence: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 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
	ENST00000648353.1	n.525+75796C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.152 AC: 23068 AN: 151940 Hom.: 1780 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0469

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.152 AC: 23077 AN: 152058 Hom.: 1778 Cov.: 32 AF XY: 0.154 AC XY: 11458 AN XY: 74338

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0456

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0872 Hom.: 192

Bravo AF: 0.151

Asia WGS AF: 0.130 AC: 453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16922328; hg19: chr11-95381168;