ENST00000753885.1:n.207+15264G>A

Variant names:

• chr1-185453472-G-A
• rs10911736
• ENST00000753885.1:n.207+15264G>A

Variant summary

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

The ENST00000753885.1(ENSG00000298206):​n.207+15264G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 152,008 control chromosomes in the GnomAD database, including 5,604 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 0.26 (5604 hom., cov: 32)
• Consequence: ENSG00000298206 ENST00000753885.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 3 publications found

Genes affected

ENSG00000298206 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753885.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298206	ENST00000753885.1		n.207+15264G>A		intron	N/A
	ENSG00000298206	ENST00000753886.1		n.110+32787G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39789 AN: 151890 Hom.: 5608 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.262 AC: 39786 AN: 152008 Hom.: 5604 Cov.: 32 AF XY: 0.261 AC XY: 19385 AN XY: 74288

African (AFR) AF: 0.209 AC: 8677 AN: 41446

American (AMR) AF: 0.192 AC: 2938 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.107 AC: 553 AN: 5152

South Asian (SAS) AF: 0.239 AC: 1149 AN: 4808

European-Finnish (FIN) AF: 0.364 AC: 3846 AN: 10554

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21033 AN: 67978

Other (OTH) AF: 0.244 AC: 515 AN: 2108

Alfa AF: 0.283 Hom.: 10497

Bravo AF: 0.245

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.4
DANN	Benign	0.67
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10911736; hg19: chr1-185422604;