rs180242

Variant names:

• chr7-93920284-T-A
• rs180242
• ENST00000820276.1:n.301-7960A>T

Variant summary

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

The ENST00000820276.1(ENSG00000306701):​n.301-7960A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,056 control chromosomes in the GnomAD database, including 29,338 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 0.62 (29338 hom., cov: 33)
• Consequence: ENSG00000306701 ENST00000820276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461
• Publications: 19 publications found

Genes affected

ENSG00000306701 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000820276.1. 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
	ENSG00000306701	ENST00000820276.1		n.301-7960A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93504 AN: 151938 Hom.: 29328 Cov.: 33

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.765

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.615 AC: 93541 AN: 152056 Hom.: 29338 Cov.: 33 AF XY: 0.620 AC XY: 46123 AN XY: 74334

African (AFR) AF: 0.488 AC: 20232 AN: 41432

American (AMR) AF: 0.626 AC: 9569 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2378 AN: 3472

East Asian (EAS) AF: 0.768 AC: 3979 AN: 5178

South Asian (SAS) AF: 0.618 AC: 2983 AN: 4826

European-Finnish (FIN) AF: 0.740 AC: 7826 AN: 10572

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44390 AN: 67962

Other (OTH) AF: 0.614 AC: 1297 AN: 2114

Alfa AF: 0.529 Hom.: 1653

Bravo AF: 0.603

Asia WGS AF: 0.629 AC: 2189 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.54
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs180242; hg19: chr7-93549596;