chr11-69639217-A-C

Variant names:

• chr11-69639217-A-C
• rs36225067
• ENST00000754571.1:n.84A>C

Variant summary

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

The ENST00000754571.1(ENSG00000298300):​n.84A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0423 in 151,998 control chromosomes in the GnomAD database, including 204 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 0.042 (204 hom., cov: 32)
• Consequence: ENSG00000298300 ENST00000754571.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.785
• Publications: 8 publications found

Genes affected

ENSG00000298300 (HGNC:58269):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0937 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
ENSG00000298300	ENST00000754571.1	n.84A>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0423 AC: 6421 AN: 151880 Hom.: 203 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0347

Gnomad ASJ AF: 0.0239

Gnomad EAS AF: 0.0181

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.00350

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0274

Gnomad OTH AF: 0.0527

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

GnomAD4 genome AF: 0.0423 AC: 6431 AN: 151998 Hom.: 204 Cov.: 32 AF XY: 0.0425 AC XY: 3160 AN XY: 74294

African (AFR) AF: 0.0772 AC: 3199 AN: 41436

American (AMR) AF: 0.0347 AC: 530 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0239 AC: 83 AN: 3472

East Asian (EAS) AF: 0.0177 AC: 91 AN: 5136

South Asian (SAS) AF: 0.101 AC: 487 AN: 4814

European-Finnish (FIN) AF: 0.00350 AC: 37 AN: 10576

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0274 AC: 1864 AN: 67956

Other (OTH) AF: 0.0555 AC: 117 AN: 2110

Alfa AF: 0.0407 Hom.: 23

Bravo AF: 0.0441

Asia WGS AF: 0.0850 AC: 298 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	15
DANN	Benign	0.75
PhyloP100		0.79

Splicing

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

Other links and lift over

dbSNP: rs36225067; hg19: chr11-69453985;