6-833579-A-G

Variant names:

• chr6-833579-A-G
• rs2317222
• ENST00000774332.1:n.625-586A>G

Variant summary

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

The ENST00000774332.1(ENSG00000271727):​n.625-586A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,098 control chromosomes in the GnomAD database, including 5,474 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 0.26 (5474 hom., cov: 32)
• Consequence: ENSG00000271727 ENST00000774332.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.264
• Publications: 7 publications found

Genes affected

ENSG00000271727 (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 = 0.381 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
ENSG00000271727	ENST00000774332.1	n.625-586A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38776 AN: 151980 Hom.: 5463 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.255 AC: 38827 AN: 152098 Hom.: 5474 Cov.: 32 AF XY: 0.256 AC XY: 19034 AN XY: 74360

African (AFR) AF: 0.362 AC: 15022 AN: 41478

American (AMR) AF: 0.224 AC: 3419 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.168 AC: 583 AN: 3468

East Asian (EAS) AF: 0.395 AC: 2043 AN: 5170

South Asian (SAS) AF: 0.251 AC: 1209 AN: 4824

European-Finnish (FIN) AF: 0.208 AC: 2200 AN: 10568

Middle Eastern (MID) AF: 0.140 AC: 41 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13717 AN: 67986

Other (OTH) AF: 0.244 AC: 516 AN: 2114

Alfa AF: 0.220 Hom.: 15076

Bravo AF: 0.260

Asia WGS AF: 0.298 AC: 1032 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.46
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2317222; hg19: chr6-833579;