7-1118508-A-T

Variant names:

• chr7-1118508-A-T
• rs11972731
• NM_001318252.2:c.129+8749T>A

Variant summary

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

The NM_001318252.2(CHLSN):​c.129+8749T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0408 in 152,234 control chromosomes in the GnomAD database, including 314 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 0.041 (314 hom., cov: 32)
• Consequence: CHLSN NM_001318252.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342
• Publications: 2 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]

LOC102723758 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001318252.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHLSN	NM_001318252.2	MANE Select	c.129+8749T>A		intron	N/A	NP_001305181.1	Q9BRJ6
	CHLSN	NM_001424325.1		c.129+8749T>A		intron	N/A	NP_001411254.1
	CHLSN	NM_001424326.1		c.129+8749T>A		intron	N/A	NP_001411255.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CHLSN	ENST00000397098.8	TSL:1 MANE Select	c.129+8749T>A		intron	N/A	ENSP00000380286.3	Q9BRJ6
	CHLSN	ENST00000357429.10	TSL:1	c.129+8749T>A		intron	N/A	ENSP00000350011.5	Q9BRJ6
	CHLSN	ENST00000397100.6	TSL:3	c.129+8749T>A		intron	N/A	ENSP00000380288.2	Q9BRJ6

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6187 AN: 152116 Hom.: 309 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0232

Gnomad ASJ AF: 0.00866

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.0205

Gnomad FIN AF: 0.00725

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00570

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0408 AC: 6208 AN: 152234 Hom.: 314 Cov.: 32 AF XY: 0.0397 AC XY: 2955 AN XY: 74444

African (AFR) AF: 0.121 AC: 5042 AN: 41500

American (AMR) AF: 0.0231 AC: 353 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00866 AC: 30 AN: 3466

East Asian (EAS) AF: 0.0206 AC: 107 AN: 5186

South Asian (SAS) AF: 0.0203 AC: 98 AN: 4826

European-Finnish (FIN) AF: 0.00725 AC: 77 AN: 10614

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00570 AC: 388 AN: 68028

Other (OTH) AF: 0.0463 AC: 98 AN: 2116

Alfa AF: 0.00788 Hom.: 5

Bravo AF: 0.0462

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.8
DANN	Benign	0.75
PhyloP100		0.34
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs11972731; hg19: chr7-1158144;