chr7-93920344-T-C

Variant names:

• chr7-93920344-T-C
• rs180241
• ENST00000820276.1:n.301-8020A>G

Variant summary

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

The ENST00000820276.1(ENSG00000306701):​n.301-8020A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.792 in 152,184 control chromosomes in the GnomAD database, including 47,879 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 0.79 (47879 hom., cov: 32)
• Consequence: ENSG00000306701 ENST00000820276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.882 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.301-8020A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120427 AN: 152066 Hom.: 47843 Cov.: 32

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.798

Gnomad EAS AF: 0.904

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.792 AC: 120511 AN: 152184 Hom.: 47879 Cov.: 32 AF XY: 0.795 AC XY: 59124 AN XY: 74386

African (AFR) AF: 0.830 AC: 34442 AN: 41518

American (AMR) AF: 0.822 AC: 12576 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.798 AC: 2770 AN: 3472

East Asian (EAS) AF: 0.903 AC: 4676 AN: 5176

South Asian (SAS) AF: 0.752 AC: 3623 AN: 4816

European-Finnish (FIN) AF: 0.790 AC: 8361 AN: 10580

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.756 AC: 51439 AN: 68006

Other (OTH) AF: 0.791 AC: 1668 AN: 2110

Alfa AF: 0.765 Hom.: 51416

Bravo AF: 0.797

Asia WGS AF: 0.814 AC: 2831 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.9
DANN	Benign	0.42
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs180241; hg19: chr7-93549656;