chr6-31290364-G-A

Variant names:

• chr6-31290364-G-A
• rs28367594
• ENST00000755297.1:n.32+19258G>A

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+19258G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0519 in 152,276 control chromosomes in the GnomAD database, including 275 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 0.052 (275 hom., cov: 33)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 6 publications found

Genes affected

ENSG00000298396 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0908 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
ENSG00000298396	ENST00000755297.1	n.32+19258G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0519 AC: 7904 AN: 152158 Hom.: 275 Cov.: 33

Gnomad AFR AF: 0.0934

Gnomad AMI AF: 0.0176

Gnomad AMR AF: 0.0653

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0269

Gnomad FIN AF: 0.00292

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0385

Gnomad OTH AF: 0.0641

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

GnomAD4 genome AF: 0.0519 AC: 7906 AN: 152276 Hom.: 275 Cov.: 33 AF XY: 0.0503 AC XY: 3742 AN XY: 74460

African (AFR) AF: 0.0933 AC: 3873 AN: 41528

American (AMR) AF: 0.0653 AC: 998 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0228 AC: 79 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0267 AC: 129 AN: 4826

European-Finnish (FIN) AF: 0.00292 AC: 31 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0385 AC: 2620 AN: 68030

Other (OTH) AF: 0.0634 AC: 134 AN: 2112

Alfa AF: 0.0459 Hom.: 201

Bravo AF: 0.0607

Asia WGS AF: 0.0200 AC: 73 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.42
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs28367594; hg19: chr6-31258141;