7-1118508-A-T

Variant summary

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

The NM_001318252.2(C7orf50):c.129+8749T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 152,234 control chromosomes in the GnomAD database, including 314 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 0.041 (314 hom., cov: 32)
• Consequence: C7orf50 NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

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

LOC102723758 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf50	NM_001318252.2	c.129+8749T>A		intron_variant		ENST00000397098.8
LOC102723758	XR_007060183.1	n.5734A>T		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf50	ENST00000397098.8	c.129+8749T>A		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6187 AN: 152116 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.00866

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00570

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0408 AC: 6208 AN: 152234 Hom.: 314 Cov.: 32 AF XY: 0.0397 AC XY: 2955 AN XY: 74444

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.0231

Gnomad4 ASJ AF: 0.00866

Gnomad4 EAS AF: 0.0206

Gnomad4 SAS AF: 0.0203

Gnomad4 FIN AF: 0.00725

Gnomad4 NFE AF: 0.00570

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.00788 Hom.: 5

Bravo AF: 0.0462

Asia WGS AF: 0.0230 AC: 79 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	5.8
Dann	Benign	0.75
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11972731; hg19: chr7-1158144;