X-110695977-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001143981.2(CHRDL1):c.610-1646A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 111,075 control chromosomes in the GnomAD database, including 11,290 homozygotes. There are 15,387 hemizygotes in GnomAD. 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 (11290 hom., 15387 hem., cov: 23)
• Consequence: CHRDL1 NM_001143981.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

Genes affected

CHRDL1 (HGNC:29861): (chordin like 1) This gene encodes an antagonist of bone morphogenetic protein 4. The encoded protein may play a role in topographic retinotectal projection and in the regulation of retinal angiogenesis in response to hypoxia. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRDL1	NM_001143981.2	c.610-1646A>C		intron_variant		ENST00000372042.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRDL1	ENST00000372042.6	c.610-1646A>C		intron_variant		2	NM_001143981.2	A1

Frequencies

GnomAD3 genomes AF: 0.485 AC: 53819 AN: 111027 Hom.: 11287 Cov.: 23 AF XY: 0.460 AC XY: 15357 AN XY: 33361

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.00952

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.485 AC: 53851 AN: 111075 Hom.: 11290 Cov.: 23 AF XY: 0.460 AC XY: 15387 AN XY: 33419

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.00955

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.420

Alfa AF: 0.386 Hom.: 39412

Bravo AF: 0.492

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.1
Dann	Benign	0.78

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: rs5943057; hg19: chrX-109939205;