rs12701220

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001424325.1(CHLSN):​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: CHLSN NM_001424325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 15 publications found

Genes affected

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

ENSG00000310291 (HGNC:):

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

Our verdict: Benign. The variant received -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
ENSG00000310291	ENST00000848853.1	n.141-4031A>G		intron_variant	Intron 1 of 3
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

African (AFR) AF: 0.0723 AC: 1128 AN: 15606

American (AMR) AF: 0.256 AC: 3154 AN: 12336

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 1414 AN: 13136

East Asian (EAS) AF: 0.354 AC: 9175 AN: 25920

South Asian (SAS) AF: 0.142 AC: 4512 AN: 31752

European-Finnish (FIN) AF: 0.283 AC: 7695 AN: 27176

Middle Eastern (MID) AF: 0.126 AC: 293 AN: 2324

European-Non Finnish (NFE) AF: 0.204 AC: 115184 AN: 563434

Other (OTH) AF: 0.181 AC: 5942 AN: 32856

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

African (AFR) AF: 0.0817 AC: 3350 AN: 40984

American (AMR) AF: 0.222 AC: 3366 AN: 15154

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 396 AN: 3436

East Asian (EAS) AF: 0.306 AC: 1506 AN: 4926

South Asian (SAS) AF: 0.143 AC: 658 AN: 4612

European-Finnish (FIN) AF: 0.291 AC: 2935 AN: 10094

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 290

European-Non Finnish (NFE) AF: 0.202 AC: 13526 AN: 67056

Other (OTH) AF: 0.169 AC: 351 AN: 2080

Alfa AF: 0.185 Hom.: 3899

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
PhyloP100		0.12
PromoterAI		-0.054	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12701220; hg19: chr7-1022728;