chr1-147252286-C-T

Position:

• chr1-147252286-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_004284.6(CHD1L):​c.128-337C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,142 control chromosomes in the GnomAD database, including 2,553 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.16 (2553 hom., cov: 32)
• Consequence: CHD1L NM_004284.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.373

Genes affected

CHD1L (HGNC:1916): (chromodomain helicase DNA binding protein 1 like) This gene encodes a DNA helicase protein involved in DNA repair. The protein converts ATP to add poly(ADP-ribose) as it regulates chromatin relaxation following DNA damage. Overexpression of this gene has been linked to several types of cancers. [provided by RefSeq, Feb 2017]

ENSG00000237188 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 1-147252286-C-T is Benign according to our data. Variant chr1-147252286-C-T is described in ClinVar as [Benign]. Clinvar id is 1268291.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CHD1L	NM_004284.6	c.128-337C>T		intron_variant		ENST00000369258.8	NP_004275.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CHD1L	ENST00000369258.8	c.128-337C>T		intron_variant		1	NM_004284.6	ENSP00000358262.4

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23690 AN: 152024 Hom.: 2540 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.0727

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.156 AC: 23744 AN: 152142 Hom.: 2553 Cov.: 32 AF XY: 0.161 AC XY: 11978 AN XY: 74378

Gnomad4 AFR AF: 0.254

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0727

Gnomad4 OTH AF: 0.155

Alfa AF: 0.112 Hom.: 319

Bravo AF: 0.167

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.88
DANN	Benign	0.19

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

Publications

LitVar

Other links and lift over

dbSNP: rs1890038; hg19: chr1-146723941; COSMIC: COSV63614074;