chr7-12508291-C-T

Variant names:

• chr7-12508291-C-T
• rs10249671
• NM_001386514.1:c.3+3745C>T

Variant summary

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

The NM_001386514.1(C7orf78):​c.3+3745C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 151,834 control chromosomes in the GnomAD database, including 7,164 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 0.29 (7164 hom., cov: 32)
• Consequence: C7orf78 NM_001386514.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• Publications: 8 publications found

Genes affected

C7orf78 (HGNC:55185):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C7orf78	NM_001386514.1	c.3+3745C>T		intron_variant	Intron 1 of 5	ENST00000636804.2	NP_001373443.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7orf78	ENST00000636804.2	c.3+3745C>T		intron_variant	Intron 1 of 5	5	NM_001386514.1	ENSP00000490444.1

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44468 AN: 151716 Hom.: 7152 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.293 AC: 44507 AN: 151834 Hom.: 7164 Cov.: 32 AF XY: 0.291 AC XY: 21627 AN XY: 74214

African (AFR) AF: 0.429 AC: 17742 AN: 41382

American (AMR) AF: 0.186 AC: 2838 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 792 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1043 AN: 5168

South Asian (SAS) AF: 0.193 AC: 929 AN: 4810

European-Finnish (FIN) AF: 0.305 AC: 3201 AN: 10508

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17225 AN: 67950

Other (OTH) AF: 0.247 AC: 520 AN: 2106

Alfa AF: 0.264 Hom.: 17533

Bravo AF: 0.292

Asia WGS AF: 0.201 AC: 697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.74
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs10249671; hg19: chr7-12547917;