rs7780687

Variant names:

• chr7-17366094-A-G
• rs7780687
• ENST00000637807.1:c.2373+25866A>G

Variant summary

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

The ENST00000637807.1(ENSG00000283321):​c.2373+25866A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.248 in 152,100 control chromosomes in the GnomAD database, including 5,439 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 0.25 (5439 hom., cov: 32)
• Consequence: ENSG00000283321 ENST00000637807.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14
• Publications: 7 publications found

Genes affected

ENSG00000283321 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637807.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283321	ENST00000637807.1	TSL:5	c.2373+25866A>G		intron	N/A	ENSP00000490530.1	A0A1B0GVI7

Frequencies

GnomAD3 genomes AF: 0.248 AC: 37652 AN: 151982 Hom.: 5424 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.248 AC: 37712 AN: 152100 Hom.: 5439 Cov.: 32 AF XY: 0.246 AC XY: 18288 AN XY: 74352

African (AFR) AF: 0.398 AC: 16500 AN: 41478

American (AMR) AF: 0.192 AC: 2933 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 593 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2034 AN: 5168

South Asian (SAS) AF: 0.194 AC: 933 AN: 4800

European-Finnish (FIN) AF: 0.163 AC: 1730 AN: 10582

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12320 AN: 67988

Other (OTH) AF: 0.232 AC: 491 AN: 2114

Alfa AF: 0.197 Hom.: 5188

Bravo AF: 0.259

Asia WGS AF: 0.256 AC: 890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7780687;

hg19: chr7-17405718;