11-95585996-G-A

Position:

• chr11-95585996-G-A

Variant summary

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

The ENST00000648353.1(ENSG00000285842):​n.525+13788G>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 0.285 in 151,554 control chromosomes in the GnomAD database, including 6,354 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 0.28 (6354 hom., cov: 31)
• Consequence: ENST00000648353.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.401 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
	ENST00000648353.1	n.525+13788G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43119 AN: 151436 Hom.: 6338 Cov.: 31

Gnomad AFR AF: 0.289

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.285 AC: 43180 AN: 151554 Hom.: 6354 Cov.: 31 AF XY: 0.288 AC XY: 21300 AN XY: 74034

Gnomad4 AFR AF: 0.289

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.281

Alfa AF: 0.201 Hom.: 592

Asia WGS AF: 0.375 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.58
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1255537; hg19: chr11-95319160; COSMIC: COSV70883306;