rs548188217

Variant names:

• chr1-15289642-C-A
• rs548188217
• NM_001391957.1:c.544C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-15289642-C-A
• chr1-15289642-C-G
• chr1-15289642-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001391957.1(FHAD1):​c.544C>A​(p.Arg182Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R182C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FHAD1 NM_001391957.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.01
• Publications: 0 publications found

Genes affected

FHAD1 (HGNC:29408): (forkhead associated phosphopeptide binding domain 1)

LOC124903853 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.0768719).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001391957.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHAD1	NM_001391957.1	MANE Select	c.544C>A	p.Arg182Ser	missense	Exon 4 of 34	NP_001378886.1	A0A804HIA4
	FHAD1	NM_052929.2		c.544C>A	p.Arg182Ser	missense	Exon 4 of 31	NP_443161.1	B1AJZ9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHAD1	ENST00000688493.1	MANE Select	c.544C>A	p.Arg182Ser	missense	Exon 4 of 34	ENSP00000509124.1	A0A804HIA4
	FHAD1	ENST00000683790.1		c.544C>A	p.Arg182Ser	missense	Exon 4 of 34	ENSP00000506973.1	A0A804HIA4
	FHAD1	ENST00000968213.1		c.544C>A	p.Arg182Ser	missense	Exon 4 of 32	ENSP00000638272.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Benign	-0.28	T
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.0
DANN	Benign	0.93
DEOGEN2	Benign	0.0013	T
Eigen	Benign	-0.72
Eigen_PC	Benign	-0.70
FATHMM_MKL	Benign	0.13	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.014	T
MetaRNN	Benign	0.077	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.0	N
PhyloP100		3.0
PrimateAI	Benign	0.21	T
PROVEAN	Benign	0.14	N
REVEL	Benign	0.090
Sift	Benign	0.84	T
Sift4G	Benign	0.48	T
Polyphen		0.15	B
Vest4		0.053
MutPred		0.36		Loss of MoRF binding (P = 0.0338)
MVP		0.055
ClinPred		0.17	T
GERP RS		3.8
Varity_R		0.077
gMVP		0.23
Mutation Taster		=97/3	polymorphism

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

Other links and lift over

dbSNP: rs548188217; hg19: chr1-15616138;