rs4075106

Positions:

• chr12-7397590-G-A
• chr12-7397590-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD163L1	NM_174941.6	c.1729+674C>T		intron_variant		ENST00000313599.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD163L1	ENST00000313599.8	c.1729+674C>T		intron_variant		1	NM_174941.6	P2
CD163L1	ENST00000416109.2	c.1759+674C>T		intron_variant		2		A2
CD163L1	ENST00000545926.1	c.347-1175C>T		intron_variant		4

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

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.0762

Gnomad4 ASJ AF: 0.0813

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.150

Gnomad4 FIN AF: 0.0257

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0256 Hom.: 27

Bravo AF: 0.128

Asia WGS AF: 0.183 AC: 633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.41
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs4075106; hg19: chr12-7550186;