rs6488340

Variant names:

• chr12-7483197-G-A
• rs6488340
• NM_203416.4:c.3088+170C>T

Your query was ambiguous. Multiple possible variants found:

• chr12-7483197-G-A
• chr12-7483197-G-C

Variant summary

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

The NM_203416.4(CD163):​c.3088+170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 772,760 control chromosomes in the GnomAD database, including 288,474 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 0.78 (48472 hom., cov: 30)
  • Exomes 𝑓: 0.87 (240002 hom.)
• Consequence: CD163 NM_203416.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 5 publications found

Genes affected

CD163 (HGNC:1631): (CD163 molecule) The protein encoded by this gene is a member of the scavenger receptor cysteine-rich (SRCR) superfamily, and is exclusively expressed in monocytes and macrophages. It functions as an acute phase-regulated receptor involved in the clearance and endocytosis of hemoglobin/haptoglobin complexes by macrophages, and may thereby protect tissues from free hemoglobin-mediated oxidative damage. This protein may also function as an innate immune sensor for bacteria and inducer of local inflammation. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203416.4. 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
	CD163	NM_203416.4	MANE Select	c.3088+170C>T		intron	N/A	NP_981961.2	Q86VB7-3
	CD163	NM_004244.6		c.3088+170C>T		intron	N/A	NP_004235.4
	CD163	NM_001370146.1		c.3088+170C>T		intron	N/A	NP_001357075.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD163	ENST00000432237.3	TSL:1 MANE Select	c.3088+170C>T		intron	N/A	ENSP00000403885.2	Q86VB7-3
	CD163	ENST00000359156.8	TSL:1	c.3088+170C>T		intron	N/A	ENSP00000352071.4	Q86VB7-1
	CD163	ENST00000396620.7	TSL:2	c.3187+170C>T		intron	N/A	ENSP00000379863.3	C9JHR8

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118019 AN: 152008 Hom.: 48450 Cov.: 30

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.820

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.879

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.791

GnomAD4 exome AF: 0.874 AC: 542163 AN: 620634 Hom.: 240002 Cov.: 8 AF XY: 0.874 AC XY: 281544 AN XY: 322228

African (AFR) AF: 0.487 AC: 7689 AN: 15796

American (AMR) AF: 0.791 AC: 15869 AN: 20062

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 13692 AN: 14926

East Asian (EAS) AF: 0.625 AC: 20438 AN: 32724

South Asian (SAS) AF: 0.831 AC: 41889 AN: 50414

European-Finnish (FIN) AF: 0.934 AC: 32033 AN: 34304

Middle Eastern (MID) AF: 0.880 AC: 2252 AN: 2558

European-Non Finnish (NFE) AF: 0.911 AC: 381037 AN: 418084

Other (OTH) AF: 0.858 AC: 27264 AN: 31766

GnomAD4 genome AF: 0.776 AC: 118091 AN: 152126 Hom.: 48472 Cov.: 30 AF XY: 0.778 AC XY: 57897 AN XY: 74390

African (AFR) AF: 0.498 AC: 20653 AN: 41448

American (AMR) AF: 0.800 AC: 12233 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3198 AN: 3472

East Asian (EAS) AF: 0.615 AC: 3174 AN: 5158

South Asian (SAS) AF: 0.820 AC: 3948 AN: 4812

European-Finnish (FIN) AF: 0.941 AC: 9990 AN: 10618

Middle Eastern (MID) AF: 0.873 AC: 255 AN: 292

European-Non Finnish (NFE) AF: 0.913 AC: 62085 AN: 68014

Other (OTH) AF: 0.793 AC: 1677 AN: 2114

Alfa AF: 0.838 Hom.: 11594

Bravo AF: 0.751

Asia WGS AF: 0.729 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.29
PhyloP100		0.28
PromoterAI		-0.020	Neutral
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: rs6488340; hg19: chr12-7635793;