rs7799917

Variant names:

• chr7-1101014-C-G
• rs7799917
• NM_001318252.2:c.129+26243G>C

Variant summary

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

The ENST00000397098.8(C7orf50):​c.129+26243G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,058 control chromosomes in the GnomAD database, including 17,902 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 0.48 (17902 hom., cov: 33)
• Consequence: C7orf50 ENST00000397098.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.17
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397098.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHLSN	NM_001318252.2	MANE Select	c.129+26243G>C		intron	N/A	NP_001305181.1
	CHLSN	NM_001424325.1		c.129+26243G>C		intron	N/A	NP_001411254.1
	CHLSN	NM_001424326.1		c.129+26243G>C		intron	N/A	NP_001411255.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C7orf50	ENST00000397098.8	TSL:1 MANE Select	c.129+26243G>C		intron	N/A	ENSP00000380286.3
	C7orf50	ENST00000357429.10	TSL:1	c.129+26243G>C		intron	N/A	ENSP00000350011.5
	C7orf50	ENST00000397100.6	TSL:3	c.129+26243G>C		intron	N/A	ENSP00000380288.2

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73127 AN: 151940 Hom.: 17885 Cov.: 33

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.484

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.481 AC: 73172 AN: 152058 Hom.: 17902 Cov.: 33 AF XY: 0.480 AC XY: 35664 AN XY: 74306

African (AFR) AF: 0.519 AC: 21539 AN: 41492

American (AMR) AF: 0.475 AC: 7261 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1693 AN: 5148

South Asian (SAS) AF: 0.409 AC: 1970 AN: 4818

European-Finnish (FIN) AF: 0.526 AC: 5553 AN: 10566

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32032 AN: 67952

Other (OTH) AF: 0.455 AC: 961 AN: 2114

Alfa AF: 0.487 Hom.: 2258

Bravo AF: 0.479

Asia WGS AF: 0.369 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.46
PhyloP100		-3.2
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: rs7799917; hg19: chr7-1140650;