rs9677663

Variant names:

• chr2-27749578-G-A
• rs9677663
• ENST00000813446.1:n.852-3294G>A

Variant summary

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

The ENST00000813446.1(ENSG00000289326):​n.852-3294G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 151,988 control chromosomes in the GnomAD database, including 30,958 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 0.62 (30958 hom., cov: 32)
• Consequence: ENSG00000289326 ENST00000813446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.65
• Publications: 4 publications found

Genes affected

ENSG00000289326 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 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
ENSG00000289326	ENST00000813446.1	n.852-3294G>A		intron_variant	Intron 3 of 4
ENSG00000289326	ENST00000813447.1	n.1064-3294G>A		intron_variant	Intron 2 of 4
ENSG00000289326	ENST00000813448.1	n.1088-3294G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.619 AC: 93985 AN: 151870 Hom.: 30965 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.618 AC: 93989 AN: 151988 Hom.: 30958 Cov.: 32 AF XY: 0.616 AC XY: 45746 AN XY: 74282

African (AFR) AF: 0.405 AC: 16773 AN: 41410

American (AMR) AF: 0.555 AC: 8485 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3472

East Asian (EAS) AF: 0.415 AC: 2141 AN: 5164

South Asian (SAS) AF: 0.671 AC: 3232 AN: 4814

European-Finnish (FIN) AF: 0.733 AC: 7742 AN: 10564

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50914 AN: 67964

Other (OTH) AF: 0.648 AC: 1368 AN: 2112

Alfa AF: 0.655 Hom.: 5157

Bravo AF: 0.590

Asia WGS AF: 0.518 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.4
DANN	Benign	0.47
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs9677663; hg19: chr2-27972445;