chr7-17366094-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375171	XR_927074.3	n.131-1697T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283321	ENST00000637807.1	c.2373+25866A>G		intron_variant	Intron 10 of 11	5		ENSP00000490530.1

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 v4.3

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

Other links and lift over

dbSNP: rs7780687; hg19: chr7-17405718;