rs11763020

chr7-1020652-C-T

Variant summary

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

The NM_001318252.2(C7orf50):c.130-10509G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,242 control chromosomes in the GnomAD database, including 1,287 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 0.12 (1287 hom., cov: 33)
• Consequence: C7orf50 NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf50	NM_001318252.2	c.130-10509G>A		intron_variant		ENST00000397098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf50	ENST00000397098.8	c.130-10509G>A		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18671 AN: 152124 Hom.: 1285 Cov.: 33

Gnomad AFR AF: 0.0722

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00655

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.123 AC: 18669 AN: 152242 Hom.: 1287 Cov.: 33 AF XY: 0.122 AC XY: 9111 AN XY: 74438

Gnomad4 AFR AF: 0.0720

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.00657

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.125

Alfa AF: 0.153 Hom.: 1835

Bravo AF: 0.118

Asia WGS AF: 0.0590 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	6.7
Dann	Benign	0.17

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: rs11763020; hg19: chr7-1060288;