rs7799917

Positions:

• chr7-1101014-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001318252.2(C7orf50):​c.129+26243G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,058 control chromosomes in the GnomAD database, including 17,902 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 0.48 (17902 hom., cov: 33)
• Consequence: C7orf50 NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17

Genes affected

C7orf50 (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf50	NM_001318252.2	c.129+26243G>C		intron_variant		ENST00000397098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf50	ENST00000397098.8	c.129+26243G>C		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73127 AN: 151940 Hom.: 17885 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.481 AC: 73172 AN: 152058 Hom.: 17902 Cov.: 33 AF XY: 0.480 AC XY: 35664 AN XY: 74306

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.455

Alfa AF: 0.487 Hom.: 2258

Bravo AF: 0.479

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7799917; hg19: chr7-1140650;