rs12701220

Variant names:

• chr7-983092-T-C
• rs12701220
• NM_001424325.1:c.565-4031A>G

Variant summary

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

The NM_001424325.1(C7orf50):​c.565-4031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 874,072 control chromosomes in the GnomAD database, including 19,299 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 0.18 (2709 hom., cov: 30)
  • Exomes 𝑓: 0.20 (16590 hom.)
• Consequence: C7orf50 NM_001424325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

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

CYP2W1 (HGNC:20243): (cytochrome P450 family 2 subfamily W member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2W1	NM_017781.3	c.-120T>C		upstream_gene_variant		ENST00000308919.12	NP_060251.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2W1	ENST00000308919.12	c.-120T>C		upstream_gene_variant		1	NM_017781.3	ENSP00000310149.7

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26268 AN: 149412 Hom.: 2701 Cov.: 30

Gnomad AFR AF: 0.0818

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.205 AC: 148497 AN: 724540 Hom.: 16590 AF XY: 0.203 AC XY: 72600 AN XY: 358300

Gnomad4 AFR exome AF: 0.0723

Gnomad4 AMR exome AF: 0.256

Gnomad4 ASJ exome AF: 0.108

Gnomad4 EAS exome AF: 0.354

Gnomad4 SAS exome AF: 0.142

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.204

Gnomad4 OTH exome AF: 0.181

GnomAD4 genome AF: 0.176 AC: 26289 AN: 149532 Hom.: 2709 Cov.: 30 AF XY: 0.178 AC XY: 13007 AN XY: 72992

Gnomad4 AFR AF: 0.0817

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.143

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.169

Alfa AF: 0.187 Hom.: 3039

Bravo AF: 0.169

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	7.3
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12701220; hg19: chr7-1022728;