6-155876368-A-G

Variant names:

• chr6-155876368-A-G
• rs4269383
• ENST00000817237.1:n.933+33410T>C

Variant summary

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

The ENST00000817237.1(ENSG00000287092):​n.933+33410T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,794 control chromosomes in the GnomAD database, including 11,104 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 0.37 (11104 hom., cov: 32)
• Consequence: ENSG00000287092 ENST00000817237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 15 publications found

Genes affected

ENSG00000287092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101928923	XR_001744423.2	n.406-43474T>C		intron_variant	Intron 4 of 8
LOC105378072	XR_001744424.2	n.260+4814A>G		intron_variant	Intron 2 of 2
LOC105378072	XR_007059824.1	n.1480+3594A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287092	ENST00000817237.1	n.933+33410T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.372 AC: 56444 AN: 151676 Hom.: 11089 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.372 AC: 56486 AN: 151794 Hom.: 11104 Cov.: 32 AF XY: 0.381 AC XY: 28299 AN XY: 74202

African (AFR) AF: 0.345 AC: 14269 AN: 41398

American (AMR) AF: 0.429 AC: 6558 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1002 AN: 3466

East Asian (EAS) AF: 0.748 AC: 3874 AN: 5176

South Asian (SAS) AF: 0.474 AC: 2286 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4454 AN: 10524

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.337 AC: 22840 AN: 67814

Other (OTH) AF: 0.381 AC: 803 AN: 2110

Alfa AF: 0.348 Hom.: 13171

Bravo AF: 0.375

Asia WGS AF: 0.569 AC: 1964 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.48
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4269383; hg19: chr6-156197502; COSMIC: COSV52394134;