chr1-27381490-G-A

Variant names:

• chr1-27381490-G-A
• rs2504778
• NM_001330448.1:c.373+290C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330448.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD164L2	NM_001330448.1	MANE Select	c.373+290C>T		intron	N/A	NP_001317377.1
	CD164L2	NM_207397.5		c.373+290C>T		intron	N/A	NP_997280.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD164L2	ENST00000374030.3	TSL:5 MANE Select	c.373+290C>T		intron	N/A	ENSP00000363142.1
	CD164L2	ENST00000374027.7	TSL:1	c.373+290C>T		intron	N/A	ENSP00000363139.3
	CD164L2	ENST00000966173.1		c.394C>T	p.Pro132Ser	missense	Exon 5 of 7	ENSP00000636232.1

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

African (AFR) AF: 0.490 AC: 20324 AN: 41436

American (AMR) AF: 0.892 AC: 13649 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3108 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3234 AN: 5164

South Asian (SAS) AF: 0.731 AC: 3521 AN: 4818

European-Finnish (FIN) AF: 0.862 AC: 9127 AN: 10592

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61475 AN: 67990

Other (OTH) AF: 0.794 AC: 1678 AN: 2114

Alfa AF: 0.828 Hom.: 8538

Bravo AF: 0.762

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs2504778; hg19: chr1-27707980;