12-7397590-G-A

Variant names:

• chr12-7397590-G-A
• rs4075106
• NM_174941.6:c.1729+674C>T

Variant summary

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

The NM_174941.6(CD163L1):​c.1729+674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,078 control chromosomes in the GnomAD database, including 1,974 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 0.12 (1974 hom., cov: 32)
• Consequence: CD163L1 NM_174941.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 2 publications found

Genes affected

CD163L1 (HGNC:30375): (CD163 molecule like 1) This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. The SRCR family is defined by a 100-110 amino acid SRCR domain, which may mediate protein-protein interaction and ligand binding. The encoded protein contains twelve SRCR domains, a transmembrane region and a cytoplasmic domain. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

CD163L1 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.281 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174941.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD163L1	NM_174941.6	MANE Select	c.1729+674C>T		intron	N/A	NP_777601.3
	CD163L1	NM_001297650.2		c.1759+674C>T		intron	N/A	NP_001284579.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD163L1	ENST00000313599.8	TSL:1 MANE Select	c.1729+674C>T		intron	N/A	ENSP00000315945.3
	CD163L1	ENST00000416109.2	TSL:2	c.1759+674C>T		intron	N/A	ENSP00000393474.2
	CD163L1	ENST00000545926.1	TSL:4	c.347-1175C>T		intron	N/A	ENSP00000439921.1

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17731 AN: 151960 Hom.: 1972 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0762

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0257

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0345

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.117 AC: 17760 AN: 152078 Hom.: 1974 Cov.: 32 AF XY: 0.115 AC XY: 8555 AN XY: 74356

African (AFR) AF: 0.285 AC: 11819 AN: 41408

American (AMR) AF: 0.0762 AC: 1165 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3468

East Asian (EAS) AF: 0.179 AC: 926 AN: 5160

South Asian (SAS) AF: 0.150 AC: 725 AN: 4818

European-Finnish (FIN) AF: 0.0257 AC: 273 AN: 10612

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2350 AN: 68016

Other (OTH) AF: 0.101 AC: 213 AN: 2112

Alfa AF: 0.0315 Hom.: 51

Bravo AF: 0.128

Asia WGS AF: 0.183 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.41
DANN	Benign	0.52
PhyloP100		-2.0
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: rs4075106; hg19: chr12-7550186;