rs2543958

Variant names:

• chr22-18890274-T-G
• rs2543958
• ENST00000614596.2:n.80-3277A>C

Variant summary

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

The ENST00000614596.2(FAM230F):​n.80-3277A>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 ENST00000614596.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 10 publications found

Genes affected

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

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: ENST00000614596.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM230F	NR_136571.2		n.104-3277A>C		intron	N/A
	FAM230F	NR_165500.3		n.137-3277A>C		intron	N/A
	FAM230F	NR_165501.3		n.109+2589A>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM230F	ENST00000614596.2	TSL:5	n.80-3277A>C		intron	N/A
	FAM230F	ENST00000717513.1		n.108-3277A>C		intron	N/A
	FAM230F	ENST00000717514.1		n.104+2589A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000683 AC: 91 AN: 133268 Hom.: 0 Cov.: 17

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: 93 AN: 133328 Hom.: 0 Cov.: 17 AF XY: 0.000653 AC XY: 42 AN XY: 64310

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00198 AC: 70 AN: 35404

American (AMR) AF: 0.000160 AC: 2 AN: 12504

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3282

East Asian (EAS) AF: 0.000426 AC: 2 AN: 4694

South Asian (SAS) AF: 0.00 AC: 0 AN: 4230

European-Finnish (FIN) AF: 0.00116 AC: 9 AN: 7754

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 258

European-Non Finnish (NFE) AF: 0.000160 AC: 10 AN: 62600

Other (OTH) AF: 0.00 AC: 0 AN: 1790

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.112 Hom.: 1792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.70
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2543958; hg19: chr22-18877787;