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GeneBe

rs1410996

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000186(CFH):c.2237-543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151884 control chromosomes in the gnomAD Genomes database, including 16321 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 0.46 ( 16321 hom., cov: 33)

Consequence

CFH
NM_000186 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CFHNM_000186.4 linkuse as main transcriptc.2237-543G>A intron_variant ENST00000367429.9
CFHXM_047418835.1 linkuse as main transcriptc.1754-543G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CFHENST00000367429.9 linkuse as main transcriptc.2237-543G>A intron_variant 1 NM_000186.4 P2

Frequencies

GnomAD3 genomes
AF:
0.459
AC:
69713
AN:
151884
Hom.:
16321
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.532
Gnomad AMI
AF:
0.258
Gnomad AMR
AF:
0.496
Gnomad ASJ
AF:
0.522
Gnomad EAS
AF:
0.441
Gnomad SAS
AF:
0.559
Gnomad FIN
AF:
0.400
Gnomad MID
AF:
0.453
Gnomad NFE
AF:
0.408
Gnomad OTH
AF:
0.479
Alfa
AF:
0.403
Hom.:
25050
Bravo
AF:
0.466
Asia WGS
AF:
0.532
AC:
1847
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
Cadd
Benign
0.089
Dann
Benign
0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1410996; hg19: chr1-196696933;