7-48046205-G-A

Position:

• chr7-48046205-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.351-255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 150,760 control chromosomes in the GnomAD database, including 15,403 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 0.44 (15403 hom., cov: 27)
• Consequence: C7orf57 NM_001100159.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C7orf57	NM_001100159.3	c.351-255G>A		intron_variant		ENST00000348904.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C7orf57	ENST00000348904.4	c.351-255G>A		intron_variant		1	NM_001100159.3	P1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 66613 AN: 150640 Hom.: 15399 Cov.: 27

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.566

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.442 AC: 66631 AN: 150760 Hom.: 15403 Cov.: 27 AF XY: 0.445 AC XY: 32723 AN XY: 73576

Gnomad4 AFR AF: 0.304

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.566

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.412

Alfa AF: 0.483 Hom.: 26714

Bravo AF: 0.429

Asia WGS AF: 0.411 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.37

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: rs2708851; hg19: chr7-48085802;