ENST00000827669.1:n.222+27797G>A

Variant names:

• chr13-37391947-G-A
• rs2323476
• ENST00000827669.1:n.222+27797G>A

Variant summary

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

The ENST00000827669.1(ENSG00000307651):​n.222+27797G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 152,052 control chromosomes in the GnomAD database, including 14,830 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 0.42 (14830 hom., cov: 32)
• Consequence: ENSG00000307651 ENST00000827669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 0 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.765 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903159	XR_007063761.1	n.243+27797G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307651	ENST00000827669.1	n.222+27797G>A		intron_variant	Intron 2 of 3
ENSG00000307651	ENST00000827670.1	n.273+27797G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64570 AN: 151936 Hom.: 14818 Cov.: 32

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.784

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.425 AC: 64600 AN: 152052 Hom.: 14830 Cov.: 32 AF XY: 0.435 AC XY: 32347 AN XY: 74298

African (AFR) AF: 0.268 AC: 11104 AN: 41472

American (AMR) AF: 0.506 AC: 7739 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1368 AN: 3470

East Asian (EAS) AF: 0.785 AC: 4047 AN: 5156

South Asian (SAS) AF: 0.519 AC: 2505 AN: 4822

European-Finnish (FIN) AF: 0.496 AC: 5234 AN: 10556

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31127 AN: 67972

Other (OTH) AF: 0.449 AC: 948 AN: 2110

Alfa AF: 0.451 Hom.: 8262

Bravo AF: 0.422

Asia WGS AF: 0.652 AC: 2265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.18
DANN	Benign	0.46
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2323476; hg19: chr13-37966084;