ENST00000641054.1:n.269-4431C>A

Variant names:

• chr7-12482533-C-A
• rs847936
• ENST00000641054.1:n.269-4431C>A

Variant summary

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

The ENST00000641054.1(C7orf78):​n.269-4431C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.834 in 152,202 control chromosomes in the GnomAD database, including 53,334 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 0.83 (53334 hom., cov: 33)
• Consequence: C7orf78 ENST00000641054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 2 publications found

Genes affected

C7orf78 (HGNC:55185):

LOC105375156 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375156	XR_001745093.2	n.618-1546G>T		intron_variant	Intron 6 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7orf78	ENST00000641054.1	n.269-4431C>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.834 AC: 126891 AN: 152084 Hom.: 53274 Cov.: 33

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.804

Gnomad OTH AF: 0.805

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

GnomAD4 genome AF: 0.834 AC: 127005 AN: 152202 Hom.: 53334 Cov.: 33 AF XY: 0.829 AC XY: 61703 AN XY: 74404

African (AFR) AF: 0.936 AC: 38878 AN: 41556

American (AMR) AF: 0.822 AC: 12564 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2580 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4072 AN: 5176

South Asian (SAS) AF: 0.762 AC: 3680 AN: 4828

European-Finnish (FIN) AF: 0.740 AC: 7821 AN: 10572

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.804 AC: 54666 AN: 68002

Other (OTH) AF: 0.807 AC: 1705 AN: 2114

Alfa AF: 0.808 Hom.: 29513

Bravo AF: 0.846

Asia WGS AF: 0.803 AC: 2788 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs847936; hg19: chr7-12522159;