chr7-48039196-G-A

Variant names:

• chr7-48039196-G-A
• rs2348666
• NM_001100159.3:c.56-2138G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C7orf57	NM_001100159.3	c.56-2138G>A		intron_variant	Intron 2 of 8	ENST00000348904.4	NP_001093629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7orf57	ENST00000348904.4	c.56-2138G>A		intron_variant	Intron 2 of 8	1	NM_001100159.3	ENSP00000335500.3

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

African (AFR) AF: 0.603 AC: 25029 AN: 41484

American (AMR) AF: 0.416 AC: 6357 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.304 AC: 1564 AN: 5148

South Asian (SAS) AF: 0.457 AC: 2202 AN: 4822

European-Finnish (FIN) AF: 0.356 AC: 3753 AN: 10542

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28487 AN: 67950

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.436 Hom.: 2607

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
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2348666; hg19: chr7-48078793;