rs10256972

Variant names:

• chr7-999367-A-C
• rs10256972
• NM_001318252.2:c.405+1103T>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.405+1103T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 152,106 control chromosomes in the GnomAD database, including 30,463 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 0.61 (30463 hom., cov: 33)
• Consequence: CHLSN NM_001424325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 26 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001424325.1. 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.405+1103T>G		intron	N/A	NP_001305181.1
	CHLSN	NM_001424325.1		c.405+1103T>G		intron	N/A	NP_001411254.1
	CHLSN	NM_001424326.1		c.405+1103T>G		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.405+1103T>G		intron	N/A	ENSP00000380286.3
	CHLSN	ENST00000357429.10	TSL:1	c.405+1103T>G		intron	N/A	ENSP00000350011.5
	CHLSN	ENST00000397100.6	TSL:3	c.405+1103T>G		intron	N/A	ENSP00000380288.2

Frequencies

GnomAD3 genomes AF: 0.613 AC: 93151 AN: 151986 Hom.: 30398 Cov.: 33

Gnomad AFR AF: 0.848

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.613 AC: 93265 AN: 152106 Hom.: 30463 Cov.: 33 AF XY: 0.609 AC XY: 45297 AN XY: 74348

African (AFR) AF: 0.848 AC: 35186 AN: 41488

American (AMR) AF: 0.612 AC: 9359 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1505 AN: 3472

East Asian (EAS) AF: 0.427 AC: 2210 AN: 5172

South Asian (SAS) AF: 0.488 AC: 2351 AN: 4818

European-Finnish (FIN) AF: 0.515 AC: 5441 AN: 10562

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35370 AN: 67996

Other (OTH) AF: 0.575 AC: 1212 AN: 2108

Alfa AF: 0.558 Hom.: 46283

Bravo AF: 0.628

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.0
DANN	Benign	0.45
PhyloP100		-0.64
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: rs10256972; hg19: chr7-1039003;