rs709086

Variant names:

• chr3-191738431-T-C
• rs709086
• ENST00000819945.1:n.349-21083T>C

Variant summary

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

The ENST00000819945.1(ENSG00000306648):​n.349-21083T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,104 control chromosomes in the GnomAD database, including 4,292 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 0.22 (4292 hom., cov: 32)
• Consequence: ENSG00000306648 ENST00000819945.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 3 publications found

Genes affected

ENSG00000306648 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000819945.1. 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
	ENSG00000306648	ENST00000819945.1		n.349-21083T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33754 AN: 151986 Hom.: 4285 Cov.: 32

Gnomad AFR AF: 0.0866

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.222 AC: 33772 AN: 152104 Hom.: 4292 Cov.: 32 AF XY: 0.228 AC XY: 16916 AN XY: 74326

African (AFR) AF: 0.0864 AC: 3587 AN: 41536

American (AMR) AF: 0.229 AC: 3505 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 876 AN: 3466

East Asian (EAS) AF: 0.315 AC: 1621 AN: 5150

South Asian (SAS) AF: 0.305 AC: 1467 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3288 AN: 10564

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18496 AN: 67970

Other (OTH) AF: 0.223 AC: 471 AN: 2114

Alfa AF: 0.253 Hom.: 16215

Bravo AF: 0.212

Asia WGS AF: 0.324 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.4
DANN	Benign	0.32
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs709086; hg19: chr3-191456220;