NM_001145268.2:c.39C>G

Variant names:

• chr7-102749246-C-G
• NM_001145268.2:c.39C>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 2P and 6B. PM2 BP4_Strong BP6_Moderate

The NM_001145268.2(FAM185A):​c.39C>G​(p.Phe13Leu) 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. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FAM185A NM_001145268.2 missense
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0270
• Publications: 0 publications found

Genes affected

FAM185A (HGNC:22412): (family with sequence similarity 185 member A)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.025468409).
• BP6: Variant 7-102749246-C-G is Benign according to our data. Variant chr7-102749246-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 3511958.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001145268.2. 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
	FAM185A	NM_001145268.2	MANE Select	c.39C>G	p.Phe13Leu	missense	Exon 1 of 8	NP_001138740.2	Q8N0U4-1
	FAM185A	NM_001350987.2		c.39C>G	p.Phe13Leu	missense	Exon 1 of 7	NP_001337916.2
	FAM185A	NM_001145269.2		c.39C>G	p.Phe13Leu	missense	Exon 1 of 7	NP_001138741.2	Q8N0U4-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM185A	ENST00000413034.3	TSL:5 MANE Select	c.39C>G	p.Phe13Leu	missense	Exon 1 of 8	ENSP00000395340.2	Q8N0U4-1
	FAM185A	ENST00000950232.1		c.39C>G	p.Phe13Leu	missense	Exon 1 of 7	ENSP00000620291.1
	FAM185A	ENST00000880455.1		c.39C>G	p.Phe13Leu	missense	Exon 1 of 7	ENSP00000550514.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
BayesDel_addAF	Benign	-0.079	T
BayesDel_noAF	Benign	-0.35
CADD	Benign	1.4
DANN	Benign	0.58
DEOGEN2	Benign	0.0024	T
Eigen	Benign	-1.3
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.067	N
LIST_S2	Benign	0.48	T
M_CAP	Benign	0.015	T
MetaRNN	Benign	0.025	T
MetaSVM	Benign	-0.98	T
MutationAssessor	Benign	-1.7	N
PhyloP100		0.027
PrimateAI	Uncertain	0.56	T
PROVEAN	Benign	-0.16	N
REVEL	Benign	0.20
Sift	Benign	0.74	T
Sift4G	Benign	1.0	T
Polyphen		0.0	B
Vest4		0.054
MutPred		0.25		Gain of catalytic residue at F13 (P = 0.0184)
MVP		0.030
ClinPred		0.043	T
GERP RS		1.7
PromoterAI		-0.31	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.065
gMVP		0.37
Mutation Taster		=99/1	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

hg19: chr7-102389693;