chr11-95585996-G-A

Variant names:

• chr11-95585996-G-A
• rs1255537
• ENST00000648353.1:n.525+13788G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648353.1(ENSG00000285842):​n.525+13788G>A variant causes a intron 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: ENSG00000285842 ENST00000648353.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291
• Publications: 2 publications found

Genes affected

ENSG00000285842 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285842	ENST00000648353.1	n.525+13788G>A		intron_variant	Intron 3 of 4
ENSG00000306211	ENST00000816277.1	n.602+29064C>T		intron_variant	Intron 2 of 4
ENSG00000306211	ENST00000816278.1	n.218-16055C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.289 AC: 11948 AN: 41280

American (AMR) AF: 0.409 AC: 6216 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3464

East Asian (EAS) AF: 0.396 AC: 2024 AN: 5114

South Asian (SAS) AF: 0.311 AC: 1490 AN: 4794

European-Finnish (FIN) AF: 0.253 AC: 2662 AN: 10506

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17261 AN: 67898

Other (OTH) AF: 0.281 AC: 590 AN: 2102

Alfa AF: 0.205 Hom.: 626

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
PhyloP100		0.29

Splicing

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

Other links and lift over

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