rs6785233

Variant names:

• chr3-171039196-T-G
• rs6785233
• ENST00000655926.1:n.292-15616T>G

Variant summary

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

The ENST00000655926.1(ENSG00000286856):​n.292-15616T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,194 control chromosomes in the GnomAD database, including 5,149 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 0.19 (5149 hom., cov: 32)
• Consequence: ENSG00000286856 ENST00000655926.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 11 publications found

Genes affected

ENSG00000286856 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286856	ENST00000655926.1	n.292-15616T>G		intron_variant	Intron 2 of 2
ENSG00000286856	ENST00000834079.1	n.309+44171T>G		intron_variant	Intron 2 of 3
ENSG00000286856	ENST00000834080.1	n.476+44171T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29105 AN: 152076 Hom.: 5130 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0344

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0322

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 29163 AN: 152194 Hom.: 5149 Cov.: 32 AF XY: 0.187 AC XY: 13935 AN XY: 74434

African (AFR) AF: 0.468 AC: 19409 AN: 41450

American (AMR) AF: 0.124 AC: 1904 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 483 AN: 3470

East Asian (EAS) AF: 0.0343 AC: 178 AN: 5190

South Asian (SAS) AF: 0.148 AC: 714 AN: 4824

European-Finnish (FIN) AF: 0.0322 AC: 342 AN: 10620

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5687 AN: 68022

Other (OTH) AF: 0.168 AC: 356 AN: 2114

Alfa AF: 0.124 Hom.: 5049

Bravo AF: 0.210

Asia WGS AF: 0.109 AC: 381 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.0
DANN	Benign	0.45
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs6785233; hg19: chr3-170756985;