ENST00000812739.1:n.89-333A>G

Variant names:

• chr20-3069747-T-C
• rs3761248
• ENST00000812739.1:n.89-333A>G

Variant summary

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

The ENST00000812739.1(ENSG00000305741):​n.89-333A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,292 control chromosomes in the GnomAD database, including 1,723 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 0.14 (1723 hom., cov: 33)
• Consequence: ENSG00000305741 ENST00000812739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0880
• Publications: 17 publications found

Genes affected

ENSG00000305741 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812739.1. 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
	ENSG00000305741	ENST00000812739.1		n.89-333A>G		intron	N/A
	ENSG00000305741	ENST00000812740.1		n.300-333A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21789 AN: 152174 Hom.: 1721 Cov.: 33

Gnomad AFR AF: 0.0960

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.143 AC: 21798 AN: 152292 Hom.: 1723 Cov.: 33 AF XY: 0.142 AC XY: 10603 AN XY: 74450

African (AFR) AF: 0.0963 AC: 4003 AN: 41572

American (AMR) AF: 0.123 AC: 1882 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 675 AN: 3470

East Asian (EAS) AF: 0.161 AC: 833 AN: 5180

South Asian (SAS) AF: 0.163 AC: 787 AN: 4818

European-Finnish (FIN) AF: 0.135 AC: 1429 AN: 10618

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11435 AN: 68016

Other (OTH) AF: 0.178 AC: 377 AN: 2116

Alfa AF: 0.156 Hom.: 3300

Bravo AF: 0.140

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.7
DANN	Benign	0.83
PhyloP100		-0.088

Splicing

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

Other links and lift over

dbSNP: rs3761248; hg19: chr20-3050393;