ENST00000816733.1:n.693-3622A>C

Variant names:

• chr10-52853118-A-C
• rs1935927
• ENST00000816733.1:n.693-3622A>C

Variant summary

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

The ENST00000816733.1(ENSG00000306279):​n.693-3622A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,012 control chromosomes in the GnomAD database, including 4,628 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 0.24 (4628 hom., cov: 32)
• Consequence: ENSG00000306279 ENST00000816733.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.444
• Publications: 3 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000816733.1. 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
	ENSG00000306279	ENST00000816733.1		n.693-3622A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37020 AN: 151894 Hom.: 4620 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.244 AC: 37043 AN: 152012 Hom.: 4628 Cov.: 32 AF XY: 0.244 AC XY: 18100 AN XY: 74288

African (AFR) AF: 0.239 AC: 9916 AN: 41474

American (AMR) AF: 0.333 AC: 5080 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3472

East Asian (EAS) AF: 0.298 AC: 1537 AN: 5152

South Asian (SAS) AF: 0.223 AC: 1074 AN: 4822

European-Finnish (FIN) AF: 0.199 AC: 2100 AN: 10566

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15919 AN: 67942

Other (OTH) AF: 0.248 AC: 524 AN: 2112

Alfa AF: 0.240 Hom.: 2340

Bravo AF: 0.256

Asia WGS AF: 0.242 AC: 840 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	6.3
DANN	Benign	0.67
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs1935927; hg19: chr10-54612878;