10-52782378-G-A

Variant names:

• chr10-52782378-G-A
• rs7477069
• ENST00000816878.1:n.528C>T

Variant summary

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

The ENST00000816878.1(ENSG00000306301):​n.528C>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 0.325 in 151,828 control chromosomes in the GnomAD database, including 8,429 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 0.33 (8429 hom., cov: 31)
• Consequence: ENSG00000306301 ENST00000816878.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 7 publications found

Genes affected

ENSG00000306301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816878.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306301	ENST00000816878.1		n.528C>T		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000306301	ENST00000816881.1		n.435C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000306279	ENST00000816733.1		n.504+2835G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49393 AN: 151710 Hom.: 8430 Cov.: 31

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.342

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

GnomAD4 genome AF: 0.325 AC: 49401 AN: 151828 Hom.: 8429 Cov.: 31 AF XY: 0.326 AC XY: 24172 AN XY: 74190

African (AFR) AF: 0.222 AC: 9187 AN: 41396

American (AMR) AF: 0.353 AC: 5381 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1430 AN: 3464

East Asian (EAS) AF: 0.386 AC: 1980 AN: 5132

South Asian (SAS) AF: 0.407 AC: 1953 AN: 4800

European-Finnish (FIN) AF: 0.314 AC: 3308 AN: 10536

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 24982 AN: 67928

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.354 Hom.: 37271

Bravo AF: 0.321

Asia WGS AF: 0.355 AC: 1234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.38
PhyloP100		-2.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7477069;

hg19: chr10-54542138;