rs10256972

chr7-999367-A-C

Variant summary

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

The NM_001318252.2(C7orf50):c.405+1103T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,106 control chromosomes in the GnomAD database, including 30,463 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 0.61 (30463 hom., cov: 33)
• Consequence: C7orf50 NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf50	NM_001318252.2	c.405+1103T>G		intron_variant		ENST00000397098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf50	ENST00000397098.8	c.405+1103T>G		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93151 AN: 151986 Hom.: 30398 Cov.: 33

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.613 AC: 93265 AN: 152106 Hom.: 30463 Cov.: 33 AF XY: 0.609 AC XY: 45297 AN XY: 74348

Gnomad4 AFR AF: 0.848

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.488

Gnomad4 FIN AF: 0.515

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.575

Alfa AF: 0.533 Hom.: 25747

Bravo AF: 0.628

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.45

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: rs10256972; hg19: chr7-1039003;