1-196943816-C-A

Variant names:

• chr1-196943816-C-A
• rs200227895
• NM_005666.4:c.-65C>A

Variant summary

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

The NM_005666.4(CFHR2):​c.-65C>A variant causes a 5 prime UTR 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: 4)
  • Failed GnomAD Quality Control
• Consequence: CFHR2 NM_005666.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 0 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=-0.94).

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.-65C>A		5_prime_UTR	Exon 1 of 5	NP_005657.1	P36980-1
	CFHR2	NM_001410924.1		c.-65C>A		5_prime_UTR	Exon 1 of 4	NP_001397853.1	A0A3B3IRW0
	CFHR2	NM_001312672.1		c.-65C>A		5_prime_UTR	Exon 1 of 3	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.-65C>A		5_prime_UTR	Exon 1 of 5	ENSP00000356385.4	P36980-1
	CFHR2	ENST00000367421.5	TSL:1	c.-65C>A		5_prime_UTR	Exon 1 of 6	ENSP00000356391.4	A0A3B3IQ51
	CFHR2	ENST00000884518.1		c.-65C>A		5_prime_UTR	Exon 1 of 6	ENSP00000554577.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 17654 Hom.: 0 Cov.: 4

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 Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 17654 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 7640

African (AFR) AF: 0.00 AC: 0 AN: 1880

American (AMR) AF: 0.00 AC: 0 AN: 1760

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 542

East Asian (EAS) AF: 0.00 AC: 0 AN: 1414

South Asian (SAS) AF: 0.00 AC: 0 AN: 584

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 850

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 86

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 10098

Other (OTH) AF: 0.00 AC: 0 AN: 248

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.7
DANN	Benign	0.43
PhyloP100		-0.44
PromoterAI		-0.0079	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: rs200227895; hg19: chr1-196912946;