rs1410996

chr1-196727803-G-Achr1-196727803-G-C

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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.24

Links

CFH (HGNC:4883):

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
CFH	NM_000186.4 linkuse as main transcript	c.2237-543G>A		intron_variant		ENST00000367429.9
CFH	XM_047418835.1 linkuse as main transcript	c.1754-543G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CFH	ENST00000367429.9 linkuse as main transcript	c.2237-543G>A		intron_variant		1	NM_000186.4	P2

Frequencies

GnomAD3 genomes

AF:

0.459

AC:

69713

AN:

151884

Hom.:

16321

Cov.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over