dbSNP rs2543958: FAM230F:n.80-3277A>C (chr22-18890274-T-G) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NR_136571.2(FAM230F):n.104-3277A>C 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 0.00070 ( 0 hom., cov: 17)

Consequence

FAM230F
NR_136571.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.248

Variant links:

Genes affected

FAM230F (HGNC:52451): (family with sequence similarity 230 member F)

FAM230F links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
FAM230F	NR_136571.2 link	n.104-3277A>C	intron_variant	Intron 1 of 11
FAM230F	NR_165500.3 link	n.137-3277A>C	intron_variant	Intron 1 of 12
FAM230F	NR_165501.3 link	n.109+2589A>C	intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM230F	ENST00000614596.2 link	n.80-3277A>C		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes

AF:

0.000683

AC:

AN:

133268

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00193

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000160

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000425

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00116

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000160

Gnomad OTH

AF:

0.00

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

GnomAD4 genome

AF:

0.000698

AC:

AN:

133328

Hom.:

Cov.:

AF XY:

0.000653

AC XY:

AN XY:

64310

show subpopulations

Gnomad4 AFR

AF:

0.00198

Gnomad4 AMR

AF:

0.000160

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000426

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00116

Gnomad4 NFE

AF:

0.000160

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0931

Hom.:

379

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

5.5

DANN

Benign

0.70

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

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over