rs847915

Variant names:

• chr7-12494964-C-T
• rs847915
• NM_001386512.1:c.-154+7893C>T

Variant summary

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

The NM_001386512.1(C7orf78):​c.-154+7893C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.636 in 151,992 control chromosomes in the GnomAD database, including 31,196 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 0.64 (31196 hom., cov: 31)
• Consequence: C7orf78 NM_001386512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C7orf78	NM_001386512.1	c.-154+7893C>T		intron_variant	Intron 2 of 6		NP_001373441.1
LOC105375156	XR_001745093.2	n.277+554G>A		intron_variant	Intron 3 of 7
LOC105375156	XR_927037.3	n.277+554G>A		intron_variant	Intron 3 of 5
LOC105375156	XR_927039.3	n.277+554G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7orf78	ENST00000635746.1	c.-154+7893C>T		intron_variant	Intron 2 of 6	5		ENSP00000490721.1
C7orf78	ENST00000641054.1	n.376+7893C>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96651 AN: 151874 Hom.: 31163 Cov.: 31

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.636 AC: 96729 AN: 151992 Hom.: 31196 Cov.: 31 AF XY: 0.632 AC XY: 46975 AN XY: 74274

African (AFR) AF: 0.545 AC: 22588 AN: 41438

American (AMR) AF: 0.718 AC: 10978 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3025 AN: 5154

South Asian (SAS) AF: 0.593 AC: 2854 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6249 AN: 10564

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46366 AN: 67962

Other (OTH) AF: 0.668 AC: 1406 AN: 2106

Alfa AF: 0.671 Hom.: 30264

Bravo AF: 0.643

Asia WGS AF: 0.626 AC: 2177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.7
DANN	Benign	0.54
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs847915; hg19: chr7-12534590;