10-52818498-A-T

Variant names:

• chr10-52818498-A-T
• rs11819277
• ENST00000816733.1:n.692+7801A>T

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.692+7801A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,012 control chromosomes in the GnomAD database, including 2,611 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 0.16 (2611 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 2 publications found

Genes affected

ENSG00000306279 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 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
ENSG00000306279	ENST00000816733.1	n.692+7801A>T		intron_variant	Intron 3 of 3
ENSG00000306279	ENST00000816737.1	n.218+6024A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24920 AN: 151894 Hom.: 2606 Cov.: 32

Gnomad AFR AF: 0.0442

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.164 AC: 24924 AN: 152012 Hom.: 2611 Cov.: 32 AF XY: 0.168 AC XY: 12459 AN XY: 74294

African (AFR) AF: 0.0441 AC: 1831 AN: 41524

American (AMR) AF: 0.281 AC: 4288 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 449 AN: 3470

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5152

South Asian (SAS) AF: 0.198 AC: 954 AN: 4822

European-Finnish (FIN) AF: 0.175 AC: 1848 AN: 10550

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13795 AN: 67934

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.177 Hom.: 332

Bravo AF: 0.168

Asia WGS AF: 0.185 AC: 645 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.56
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11819277; hg19: chr10-54578258;