1-157843963-C-T

Variant names:

• chr1-157843963-C-T
• rs3761957
• ENST00000484609.1:n.265+2748G>A

Variant summary

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

The ENST00000484609.1(CD5L):​n.265+2748G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 152,152 control chromosomes in the GnomAD database, including 753 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 0.067 (753 hom., cov: 32)
• Consequence: CD5L ENST00000484609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

Genes affected

CD5L (HGNC:1690): (CD5 molecule like) Predicted to enable serine-type endopeptidase activity. Predicted to be involved in zymogen activation. Predicted to act upstream of or within positive regulation of complement-dependent cytotoxicity and regulation of complement activation. Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD5L	ENST00000484609.1	n.265+2748G>A		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.0672 AC: 10214 AN: 152036 Hom.: 754 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.0536

Gnomad FIN AF: 0.00123

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00648

Gnomad OTH AF: 0.0550

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

GnomAD4 genome AF: 0.0673 AC: 10235 AN: 152152 Hom.: 753 Cov.: 32 AF XY: 0.0683 AC XY: 5080 AN XY: 74384

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.0537

Gnomad4 FIN AF: 0.00123

Gnomad4 NFE AF: 0.00648

Gnomad4 OTH AF: 0.0545

Alfa AF: 0.00374 Hom.: 2

Bravo AF: 0.0831

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.34

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3761957; hg19: chr1-157813753;