rs6951245

Variant names:

• chr7-1018557-G-A
• rs6951245
• NM_001318252.2:c.130-8414C>T

Variant summary

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

The NM_001318252.2(CHLSN):​c.130-8414C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 151,728 control chromosomes in the GnomAD database, including 1,276 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 0.12 (1276 hom., cov: 32)
• Consequence: CHLSN NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 13 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CHLSN	NM_001318252.2	c.130-8414C>T		intron_variant	Intron 2 of 4	ENST00000397098.8	NP_001305181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C7orf50	ENST00000397098.8	c.130-8414C>T		intron_variant	Intron 2 of 4	1	NM_001318252.2	ENSP00000380286.3

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18628 AN: 151606 Hom.: 1274 Cov.: 32

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00633

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.123 AC: 18634 AN: 151728 Hom.: 1276 Cov.: 32 AF XY: 0.123 AC XY: 9088 AN XY: 74150

African (AFR) AF: 0.0760 AC: 3146 AN: 41396

American (AMR) AF: 0.111 AC: 1689 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 736 AN: 3468

East Asian (EAS) AF: 0.00635 AC: 32 AN: 5042

South Asian (SAS) AF: 0.137 AC: 657 AN: 4794

European-Finnish (FIN) AF: 0.128 AC: 1354 AN: 10582

Middle Eastern (MID) AF: 0.213 AC: 61 AN: 286

European-Non Finnish (NFE) AF: 0.156 AC: 10574 AN: 67872

Other (OTH) AF: 0.123 AC: 258 AN: 2102

Alfa AF: 0.137 Hom.: 176

Bravo AF: 0.118

Asia WGS AF: 0.0570 AC: 201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.56
DANN	Benign	0.59
PhyloP100		-1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
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: rs6951245; hg19: chr7-1058193;