ENST00000839999.1:n.282+9770A>C

Variant names:

• chr20-7793055-T-G
• rs730270
• ENST00000839999.1:n.282+9770A>C

Variant summary

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

The ENST00000839999.1(ENSG00000309276):​n.282+9770A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,200 control chromosomes in the GnomAD database, including 1,166 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 0.11 (1166 hom., cov: 32)
• Consequence: ENSG00000309276 ENST00000839999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 0 publications found

Genes affected

ENSG00000309276 (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 (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839999.1. 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
	ENSG00000309276	ENST00000839999.1		n.282+9770A>C		intron	N/A
	ENSG00000309276	ENST00000840001.1		n.319+9770A>C		intron	N/A
	ENSG00000309276	ENST00000840002.1		n.85+5194A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17273 AN: 152082 Hom.: 1159 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0341

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.114 AC: 17300 AN: 152200 Hom.: 1166 Cov.: 32 AF XY: 0.115 AC XY: 8574 AN XY: 74422

African (AFR) AF: 0.119 AC: 4943 AN: 41520

American (AMR) AF: 0.155 AC: 2364 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 618 AN: 3470

East Asian (EAS) AF: 0.157 AC: 813 AN: 5168

South Asian (SAS) AF: 0.328 AC: 1579 AN: 4816

European-Finnish (FIN) AF: 0.0483 AC: 512 AN: 10606

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6092 AN: 68018

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.0947 Hom.: 336

Bravo AF: 0.120

Asia WGS AF: 0.265 AC: 921 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	1.0
DANN	Benign	0.65
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs730270; hg19: chr20-7773702;