rs6779441

Variant names:

• chr3-118297386-A-G
• rs6779441
• ENST00000482142.5:n.232+199237T>C

Variant summary

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

The ENST00000482142.5(ENSG00000243276):​n.232+199237T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,922 control chromosomes in the GnomAD database, including 4,690 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 0.18 (4690 hom., cov: 32)
• Consequence: ENSG00000243276 ENST00000482142.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.86
• Publications: 2 publications found

Genes affected

ENSG00000243276 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 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
ENSG00000243276	ENST00000482142.5	n.232+199237T>C		intron_variant	Intron 3 of 6	5

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27296 AN: 151802 Hom.: 4676 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0848

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.180 AC: 27356 AN: 151922 Hom.: 4690 Cov.: 32 AF XY: 0.176 AC XY: 13041 AN XY: 74264

African (AFR) AF: 0.450 AC: 18625 AN: 41430

American (AMR) AF: 0.118 AC: 1803 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.0848 AC: 294 AN: 3466

East Asian (EAS) AF: 0.155 AC: 792 AN: 5126

South Asian (SAS) AF: 0.167 AC: 808 AN: 4830

European-Finnish (FIN) AF: 0.0355 AC: 377 AN: 10612

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0626 AC: 4249 AN: 67928

Other (OTH) AF: 0.173 AC: 365 AN: 2108

Alfa AF: 0.0987 Hom.: 6148

Bravo AF: 0.198

Asia WGS AF: 0.186 AC: 654 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.36
DANN	Benign	0.22
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6779441; hg19: chr3-118016233;