chr1-26161895-C-G

Variant names:

• chr1-26161895-C-G
• NM_024869.3:c.604C>G

Variant summary

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

The NM_024869.3(FAM110D):​c.604C>G​(p.Pro202Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000232 in 1,292,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000023 (0 hom.)
• Consequence: FAM110D NM_024869.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.77
• Publications: 0 publications found

Genes affected

FAM110D (HGNC:25860): (family with sequence similarity 110 member D)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.066432774).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024869.3. 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
	FAM110D	NM_024869.3	MANE Select	c.604C>G	p.Pro202Ala	missense	Exon 2 of 2	NP_079145.2	Q8TAY7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM110D	ENST00000374268.5	TSL:1 MANE Select	c.604C>G	p.Pro202Ala	missense	Exon 2 of 2	ENSP00000363386.3	Q8TAY7
	FAM110D	ENST00000880266.1		c.604C>G	p.Pro202Ala	missense	Exon 3 of 3	ENSP00000550325.1
	FAM110D	ENST00000880267.1		c.604C>G	p.Pro202Ala	missense	Exon 3 of 3	ENSP00000550326.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000232 AC: 3 AN: 1292064 Hom.: 0 Cov.: 32 AF XY: 0.00000158 AC XY: 1 AN XY: 630990

African (AFR) AF: 0.00 AC: 0 AN: 25586

American (AMR) AF: 0.00 AC: 0 AN: 21898

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20720

East Asian (EAS) AF: 0.00 AC: 0 AN: 30152

South Asian (SAS) AF: 0.00 AC: 0 AN: 66510

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32556

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4066

European-Non Finnish (NFE) AF: 0.00000193 AC: 2 AN: 1037034

Other (OTH) AF: 0.0000187 AC: 1 AN: 53542

GnomAD4 genome Cov.: 32

ClinVar

ClinVar submissions

Significance: Uncertain significance

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	0.055
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.56
CADD	Benign	17
DANN	Benign	0.80
DEOGEN2	Benign	0.00091	T
Eigen	Benign	-0.76
Eigen_PC	Benign	-0.69
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.50	T
M_CAP	Uncertain	0.14	D
MetaRNN	Benign	0.066	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.55	N
PhyloP100		1.8
PrimateAI	Pathogenic	0.79	T
PROVEAN	Benign	0.56	N
REVEL	Benign	0.056
Sift	Benign	0.69	T
Sift4G	Benign	0.87	T
Polyphen		0.0060	B
Vest4		0.15
MutPred		0.17		Loss of glycosylation at P202 (P = 0.0134)
MVP		0.082
MPC		1.0
ClinPred		0.055	T
GERP RS		3.4
Varity_R		0.084
gMVP		0.28
Mutation Taster		=94/6	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: chr1-26488386;