rs2348666

chr7-48039196-G-A

Variant summary

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

The NM_001100159.3(C7orf57):c.56-2138G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,008 control chromosomes in the GnomAD database, including 17,051 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 0.46 (17051 hom., cov: 32)
• Consequence: C7orf57 NM_001100159.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545

Genes affected

C7orf57 (HGNC:22247): (chromosome 7 open reading frame 57)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf57	NM_001100159.3	c.56-2138G>A		intron_variant		ENST00000348904.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf57	ENST00000348904.4	c.56-2138G>A		intron_variant		1	NM_001100159.3	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70576 AN: 151890 Hom.: 17022 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.465 AC: 70643 AN: 152008 Hom.: 17051 Cov.: 32 AF XY: 0.459 AC XY: 34097 AN XY: 74270

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.451

Gnomad4 EAS AF: 0.304

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.492

Alfa AF: 0.432 Hom.: 2488

Bravo AF: 0.478

Asia WGS AF: 0.376 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.0
Dann	Benign	0.69

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: rs2348666; hg19: chr7-48078793;