rs7780181

Variant names:

• chr7-137021788-T-G
• rs7780181
• ENST00000439694.6:n.655+10117A>C

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.655+10117A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,630 control chromosomes in the GnomAD database, including 15,636 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 0.45 (15636 hom., cov: 31)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 3 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439694.6. 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
	LOC349160	NR_046103.1		n.341+11006A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000234352	ENST00000439694.6	TSL:1	n.655+10117A>C		intron	N/A
	ENSG00000234352	ENST00000425981.2	TSL:2	n.341+11006A>C		intron	N/A
	ENSG00000234352	ENST00000586239.5	TSL:5	n.273+11006A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67461 AN: 151512 Hom.: 15603 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.445 AC: 67534 AN: 151630 Hom.: 15636 Cov.: 31 AF XY: 0.438 AC XY: 32457 AN XY: 74078

African (AFR) AF: 0.523 AC: 21629 AN: 41382

American (AMR) AF: 0.359 AC: 5455 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3468

East Asian (EAS) AF: 0.103 AC: 525 AN: 5118

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4822

European-Finnish (FIN) AF: 0.438 AC: 4614 AN: 10536

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31337 AN: 67806

Other (OTH) AF: 0.439 AC: 923 AN: 2102

Alfa AF: 0.445 Hom.: 12466

Bravo AF: 0.444

Asia WGS AF: 0.219 AC: 764 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.43
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs7780181; hg19: chr7-136706535;