rs2765501

Variant names:

• chr1-157834858-G-A
• rs2765501
• NM_005894.3:c.377-110C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-157834858-G-A
• chr1-157834858-G-T

Variant summary

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

The NM_005894.3(CD5L):​c.377-110C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 740,606 control chromosomes in the GnomAD database, including 56,104 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 0.31 (9248 hom., cov: 32)
  • Exomes 𝑓: 0.39 (46856 hom.)
• Consequence: CD5L NM_005894.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 18 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD5L	NM_005894.3	c.377-110C>T		intron_variant	Intron 3 of 5	ENST00000368174.5	NP_005885.1
CD5L	NM_001347698.2	c.377-110C>T		intron_variant	Intron 3 of 5		NP_001334627.1
CD5L	XM_017002806.2	c.377-110C>T		intron_variant	Intron 3 of 5		XP_016858295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD5L	ENST00000368174.5	c.377-110C>T		intron_variant	Intron 3 of 5	1	NM_005894.3	ENSP00000357156.4

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46817 AN: 151988 Hom.: 9245 Cov.: 32

Gnomad AFR AF: 0.0731

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.311

GnomAD4 exome AF: 0.387 AC: 228017 AN: 588500 Hom.: 46856 AF XY: 0.387 AC XY: 117667 AN XY: 303924

African (AFR) AF: 0.0661 AC: 1033 AN: 15634

American (AMR) AF: 0.227 AC: 4800 AN: 21174

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 4369 AN: 14802

East Asian (EAS) AF: 0.361 AC: 11651 AN: 32310

South Asian (SAS) AF: 0.360 AC: 17921 AN: 49718

European-Finnish (FIN) AF: 0.525 AC: 19645 AN: 37412

Middle Eastern (MID) AF: 0.316 AC: 764 AN: 2416

European-Non Finnish (NFE) AF: 0.408 AC: 156935 AN: 384454

Other (OTH) AF: 0.356 AC: 10899 AN: 30580

GnomAD4 genome AF: 0.308 AC: 46818 AN: 152106 Hom.: 9248 Cov.: 32 AF XY: 0.313 AC XY: 23300 AN XY: 74356

African (AFR) AF: 0.0730 AC: 3031 AN: 41546

American (AMR) AF: 0.259 AC: 3957 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1876 AN: 5160

South Asian (SAS) AF: 0.361 AC: 1739 AN: 4814

European-Finnish (FIN) AF: 0.528 AC: 5575 AN: 10562

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28519 AN: 67956

Other (OTH) AF: 0.308 AC: 651 AN: 2114

Alfa AF: 0.369 Hom.: 35514

Bravo AF: 0.275

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.074
DANN	Benign	0.46
PhyloP100		-0.74
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: rs2765501; hg19: chr1-157804648;