chr7-1044141-A-G

Variant names:

• chr7-1044141-A-G
• rs1997243
• NM_001318252.2:c.130-33998T>C

Variant summary

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

The NM_001318252.2(CHLSN):​c.130-33998T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,302 control chromosomes in the GnomAD database, including 1,160 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 0.11 (1160 hom., cov: 34)
• Consequence: CHLSN NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 75 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]

ENSG00000225146 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• 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.130-33998T>C		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.130-33998T>C		intron_variant	Intron 2 of 4	1	NM_001318252.2	ENSP00000380286.3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16318 AN: 152184 Hom.: 1158 Cov.: 34

Gnomad AFR AF: 0.0252

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.107 AC: 16317 AN: 152302 Hom.: 1160 Cov.: 34 AF XY: 0.107 AC XY: 7973 AN XY: 74472

African (AFR) AF: 0.0252 AC: 1048 AN: 41584

American (AMR) AF: 0.102 AC: 1568 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.130 AC: 627 AN: 4830

European-Finnish (FIN) AF: 0.128 AC: 1357 AN: 10618

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10557 AN: 68000

Other (OTH) AF: 0.112 AC: 237 AN: 2110

Alfa AF: 0.139 Hom.: 4955

Bravo AF: 0.100

Asia WGS AF: 0.0500 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.40
PhyloP100		0.15
PromoterAI		0.045	Neutral
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: rs1997243; hg19: chr7-1083777;