11-69639167-C-T

Variant names:

• chr11-69639167-C-T
• rs1944129
• ENST00000754571.1:n.34C>T

Variant summary

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

The ENST00000754571.1(ENSG00000298300):​n.34C>T 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 0.476 in 152,110 control chromosomes in the GnomAD database, including 17,711 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 0.48 (17711 hom., cov: 33)
• Consequence: ENSG00000298300 ENST00000754571.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 9 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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 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.34C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72328 AN: 151990 Hom.: 17699 Cov.: 33

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.476 AC: 72372 AN: 152110 Hom.: 17711 Cov.: 33 AF XY: 0.479 AC XY: 35630 AN XY: 74368

African (AFR) AF: 0.418 AC: 17335 AN: 41472

American (AMR) AF: 0.440 AC: 6721 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1843 AN: 3472

East Asian (EAS) AF: 0.824 AC: 4251 AN: 5162

South Asian (SAS) AF: 0.604 AC: 2917 AN: 4832

European-Finnish (FIN) AF: 0.445 AC: 4712 AN: 10590

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32978 AN: 67974

Other (OTH) AF: 0.499 AC: 1055 AN: 2116

Alfa AF: 0.340 Hom.: 1007

Bravo AF: 0.473

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.84
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs1944129; hg19: chr11-69453935;