rs7565678

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000286290 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000669555.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286290	ENST00000669555.1		n.587+3678A>G		intron	N/A

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

African (AFR) AF: 0.483 AC: 20010 AN: 41450

American (AMR) AF: 0.181 AC: 2759 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3472

East Asian (EAS) AF: 0.128 AC: 664 AN: 5174

South Asian (SAS) AF: 0.179 AC: 861 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1680 AN: 10586

Middle Eastern (MID) AF: 0.286 AC: 83 AN: 290

European-Non Finnish (NFE) AF: 0.180 AC: 12249 AN: 67996

Other (OTH) AF: 0.231 AC: 488 AN: 2116

Alfa AF: 0.209 Hom.: 12390

Bravo AF: 0.273

Asia WGS AF: 0.162 AC: 565 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.75
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7565678; hg19: chr2-103999574;