rs7680285

Variant names:

• chr4-180070291-A-G
• rs7680285
• ENST00000826655.1:n.74+11009A>G

Variant summary

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

The ENST00000826655.1(ENSG00000307510):​n.74+11009A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0936 in 152,076 control chromosomes in the GnomAD database, including 912 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 0.094 (912 hom., cov: 32)
• Consequence: ENSG00000307510 ENST00000826655.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 1 publications found

Genes affected

ENSG00000307510 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000826655.1. 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
	ENSG00000307510	ENST00000826655.1		n.74+11009A>G		intron	N/A
	ENSG00000307510	ENST00000826656.1		n.39+11009A>G		intron	N/A
	ENSG00000307510	ENST00000826657.1		n.33+11009A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0936 AC: 14230 AN: 151958 Hom.: 911 Cov.: 32

Gnomad AFR AF: 0.0247

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.0751

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.000580

Gnomad SAS AF: 0.0185

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.0936 AC: 14230 AN: 152076 Hom.: 912 Cov.: 32 AF XY: 0.0895 AC XY: 6653 AN XY: 74334

African (AFR) AF: 0.0247 AC: 1024 AN: 41496

American (AMR) AF: 0.0750 AC: 1146 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3466

East Asian (EAS) AF: 0.000582 AC: 3 AN: 5156

South Asian (SAS) AF: 0.0185 AC: 89 AN: 4808

European-Finnish (FIN) AF: 0.117 AC: 1240 AN: 10586

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.145 AC: 9877 AN: 67964

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.126 Hom.: 2187

Bravo AF: 0.0873

Asia WGS AF: 0.0170 AC: 61 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.054
DANN	Benign	0.54
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs7680285; hg19: chr4-180991444;