rs140103005

Variant names:

• chr1-196944067-C-A
• rs140103005
• NM_005666.4:c.58+129C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-196944067-C-A
• chr1-196944067-C-G
• chr1-196944067-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_005666.4(CFHR2):​c.58+129C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 15)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CFHR2 NM_005666.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.258
• Publications: 2 publications found

Genes affected

CFHR2 (HGNC:4890): (complement factor H related 2) This gene belongs to a family of complement factor H-related genes (CFHR), which are clustered together with complement factor H gene on chromosome 1, and are involved in regulation of complement. Mutations in CFHR genes have been associated with dense deposit disease and atypical haemolytic-uraemic syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005666.4. 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
	CFHR2	NM_005666.4	MANE Select	c.58+129C>A		intron	N/A	NP_005657.1	P36980-1
	CFHR2	NM_001410924.1		c.58+129C>A		intron	N/A	NP_001397853.1	A0A3B3IRW0
	CFHR2	NM_001312672.1		c.58+129C>A		intron	N/A	NP_001299601.1	A0A3B3IS28

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFHR2	ENST00000367415.8	TSL:1 MANE Select	c.58+129C>A		intron	N/A	ENSP00000356385.4	P36980-1
	CFHR2	ENST00000367421.5	TSL:1	c.58+129C>A		intron	N/A	ENSP00000356391.4	A0A3B3IQ51
	CFHR2	ENST00000473386.1	TSL:1	c.58+129C>A		intron	N/A	ENSP00000497089.1	A0A3B3IS28

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 96188 Hom.: 0 Cov.: 15

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 220122 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 117006

African (AFR) AF: 0.00 AC: 0 AN: 3080

American (AMR) AF: 0.00 AC: 0 AN: 11044

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5328

East Asian (EAS) AF: 0.00 AC: 0 AN: 18376

South Asian (SAS) AF: 0.00 AC: 0 AN: 24590

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 20206

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 650

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 125400

Other (OTH) AF: 0.00 AC: 0 AN: 11448

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 96188 Hom.: 0 Cov.: 15 AF XY: 0.00 AC XY: 0 AN XY: 46522

African (AFR) AF: 0.00 AC: 0 AN: 16444

American (AMR) AF: 0.00 AC: 0 AN: 9868

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2404

East Asian (EAS) AF: 0.00 AC: 0 AN: 4050

South Asian (SAS) AF: 0.00 AC: 0 AN: 2914

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 7692

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 190

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50586

Other (OTH) AF: 0.00 AC: 0 AN: 1246

Alfa AF: 0.00 Hom.: 1233

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		-0.26
PromoterAI		-0.0065	Neutral

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: rs140103005; hg19: chr1-196913197;