ENST00000840727.1:n.51-9597T>C

Variant names:

• chr1-160660353-T-C
• rs11265461
• ENST00000840727.1:n.51-9597T>C

Variant summary

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

The ENST00000840727.1(ENSG00000228863):​n.51-9597T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 151,908 control chromosomes in the GnomAD database, including 10,232 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 0.36 (10232 hom., cov: 31)
• Consequence: ENSG00000228863 ENST00000840727.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 16 publications found

Genes affected

ENSG00000228863 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.418 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
ENSG00000228863	ENST00000840727.1	n.51-9597T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55054 AN: 151790 Hom.: 10217 Cov.: 31

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.363 AC: 55117 AN: 151908 Hom.: 10232 Cov.: 31 AF XY: 0.361 AC XY: 26814 AN XY: 74252

African (AFR) AF: 0.423 AC: 17504 AN: 41390

American (AMR) AF: 0.394 AC: 6001 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2149 AN: 5180

South Asian (SAS) AF: 0.228 AC: 1099 AN: 4818

European-Finnish (FIN) AF: 0.330 AC: 3477 AN: 10552

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23152 AN: 67936

Other (OTH) AF: 0.338 AC: 713 AN: 2112

Alfa AF: 0.346 Hom.: 41802

Bravo AF: 0.372

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs11265461; hg19: chr1-160630143;