rs3862822

Variant names:

• chr6-113658599-G-A
• rs3862822
• ENST00000788590.1:n.153-18455G>A

Variant summary

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

The ENST00000788590.1(ENSG00000302660):​n.153-18455G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.852 in 152,156 control chromosomes in the GnomAD database, including 55,732 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 0.85 (55732 hom., cov: 31)
• Consequence: ENSG00000302660 ENST00000788590.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 1 publications found

Genes affected

ENSG00000302660 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.908 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
ENSG00000302660	ENST00000788590.1	n.153-18455G>A		intron_variant	Intron 1 of 1
ENSG00000302660	ENST00000788591.1	n.476+15780G>A		intron_variant	Intron 1 of 1
ENSG00000302660	ENST00000788592.1	n.477-2384G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.853 AC: 129620 AN: 152038 Hom.: 55702 Cov.: 31

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.898

Gnomad OTH AF: 0.865

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

GnomAD4 genome AF: 0.852 AC: 129707 AN: 152156 Hom.: 55732 Cov.: 31 AF XY: 0.854 AC XY: 63539 AN XY: 74394

African (AFR) AF: 0.736 AC: 30538 AN: 41476

American (AMR) AF: 0.921 AC: 14086 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3064 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4224 AN: 5176

South Asian (SAS) AF: 0.845 AC: 4075 AN: 4820

European-Finnish (FIN) AF: 0.913 AC: 9674 AN: 10592

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.898 AC: 61087 AN: 68010

Other (OTH) AF: 0.864 AC: 1822 AN: 2110

Alfa AF: 0.887 Hom.: 100227

Bravo AF: 0.852

Asia WGS AF: 0.844 AC: 2934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.46
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs3862822; hg19: chr6-113979801;