1-196688525-C-T

Variant names:

• chr1-196688525-C-T
• rs10801554
• NM_000186.4:c.965-895C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000186.4(CFH):​c.965-895C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 151,972 control chromosomes in the GnomAD database, including 32,036 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 0.64 (32036 hom., cov: 32)
• Consequence: CFH NM_000186.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492

Genes affected

CFH (HGNC:4883): (complement factor H) This gene is a member of the Regulator of Complement Activation (RCA) gene cluster and encodes a protein with twenty short consensus repeat (SCR) domains. This protein is secreted into the bloodstream and has an essential role in the regulation of complement activation, restricting this innate defense mechanism to microbial infections. Mutations in this gene have been associated with hemolytic-uremic syndrome (HUS) and chronic hypocomplementemic nephropathy. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Oct 2011]

ENSG00000289697 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CFH	NM_000186.4	c.965-895C>T		intron_variant	Intron 7 of 21	ENST00000367429.9	NP_000177.2
CFH	NM_001014975.3	c.965-895C>T		intron_variant	Intron 7 of 9		NP_001014975.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CFH	ENST00000367429.9	c.965-895C>T		intron_variant	Intron 7 of 21	1	NM_000186.4	ENSP00000356399.4
ENSG00000289697	ENST00000696032.1	c.965-895C>T		intron_variant	Intron 7 of 26			ENSP00000512341.1

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97919 AN: 151854 Hom.: 32012 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.719

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.645 AC: 97984 AN: 151972 Hom.: 32036 Cov.: 32 AF XY: 0.648 AC XY: 48099 AN XY: 74258

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.949

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.564

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.665

Alfa AF: 0.629 Hom.: 3754

Bravo AF: 0.660

Asia WGS AF: 0.780 AC: 2707 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.63

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: rs10801554; hg19: chr1-196657655;