rs2504778

chr1-27381490-G-A

Variant summary

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

The NM_001330448.1(CD164L2):c.373+290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,086 control chromosomes in the GnomAD database, including 47,769 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 0.77 (47769 hom., cov: 31)
• Consequence: CD164L2 NM_001330448.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440

Genes affected

CD164L2 (HGNC:32043): (CD164 molecule like 2) Predicted to be integral component of membrane. Predicted to be active in cytoplasmic vesicle. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD164L2	NM_001330448.1	c.373+290C>T		intron_variant		ENST00000374030.3
CD164L2	NM_207397.5	c.373+290C>T		intron_variant
CD164L2	XM_011541441.2	c.373+290C>T		intron_variant
CD164L2	XR_241190.4	n.467+290C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD164L2	ENST00000374030.3	c.373+290C>T		intron_variant		5	NM_001330448.1	A1
CD164L2	ENST00000374027.7	c.373+290C>T		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117196 AN: 151968 Hom.: 47756 Cov.: 31

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.892

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.771 AC: 117238 AN: 152086 Hom.: 47769 Cov.: 31 AF XY: 0.770 AC XY: 57290 AN XY: 74362

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.892

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.794

Alfa AF: 0.828 Hom.: 8538

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	2.9

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2504778; hg19: chr1-27707980;