rs7565678

Variant names:

• chr2-103383116-A-G
• rs7565678
• ENST00000669555.1:n.587+3678A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000669555.1(ENSG00000286290):​n.587+3678A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,098 control chromosomes in the GnomAD database, including 6,590 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 (6590 hom., cov: 32)
• Consequence: ENSG00000286290 ENST00000669555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.281

Genes affected

ENSG00000286290 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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
ENSG00000286290	ENST00000669555.1	n.587+3678A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39532 AN: 151982 Hom.: 6577 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.260 AC: 39584 AN: 152098 Hom.: 6590 Cov.: 32 AF XY: 0.256 AC XY: 19016 AN XY: 74368

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.231

Alfa AF: 0.191 Hom.: 5999

Bravo AF: 0.273

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565678; hg19: chr2-103999574;