rs6773586

Variant names:

• chr3-39309966-A-T
• rs6773586
• ENST00000655387.2:n.435-17016T>A

Variant summary

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

The ENST00000655387.2(ENSG00000287780):​n.435-17016T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,212 control chromosomes in the GnomAD database, including 3,798 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 0.20 (3798 hom., cov: 33)
• Consequence: ENSG00000287780 ENST00000655387.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 1 publications found

Genes affected

ENSG00000287780 (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 (AFR) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655387.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287780	ENST00000655387.2		n.435-17016T>A		intron	N/A
	ENSG00000287780	ENST00000836879.1		n.288-17016T>A		intron	N/A
	ENSG00000287780	ENST00000836880.1		n.373-17016T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30000 AN: 152094 Hom.: 3783 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.00865

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.197 AC: 30051 AN: 152212 Hom.: 3798 Cov.: 33 AF XY: 0.192 AC XY: 14275 AN XY: 74444

African (AFR) AF: 0.349 AC: 14472 AN: 41518

American (AMR) AF: 0.159 AC: 2431 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.00867 AC: 45 AN: 5190

South Asian (SAS) AF: 0.0474 AC: 229 AN: 4828

European-Finnish (FIN) AF: 0.112 AC: 1188 AN: 10606

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10495 AN: 68002

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.165 Hom.: 358

Bravo AF: 0.209

Asia WGS AF: 0.0530 AC: 185 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.71
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs6773586; hg19: chr3-39351457;