rs1316008005

Variant names:

• chr1-26161989-C-G
• rs1316008005
• NM_024869.3:c.698C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-26161989-C-G
• chr1-26161989-C-T

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.698C>G​(p.Ala233Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000645 in 1,086,006 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. 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. A233V) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000064 (0 hom.)
• Consequence: FAM110D NM_024869.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• 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=0.048626244).

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.698C>G	p.Ala233Gly	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.698C>G	p.Ala233Gly	missense	Exon 2 of 2	ENSP00000363386.3	Q8TAY7
	FAM110D	ENST00000880266.1		c.698C>G	p.Ala233Gly	missense	Exon 3 of 3	ENSP00000550325.1
	FAM110D	ENST00000880267.1		c.698C>G	p.Ala233Gly	missense	Exon 3 of 3	ENSP00000550326.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000645 AC: 7 AN: 1086006 Hom.: 0 Cov.: 31 AF XY: 0.00000581 AC XY: 3 AN XY: 516038

African (AFR) AF: 0.00 AC: 0 AN: 22504

American (AMR) AF: 0.00 AC: 0 AN: 8046

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13878

East Asian (EAS) AF: 0.00 AC: 0 AN: 25748

South Asian (SAS) AF: 0.00 AC: 0 AN: 20808

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21504

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3116

European-Non Finnish (NFE) AF: 0.00000755 AC: 7 AN: 926946

Other (OTH) AF: 0.00 AC: 0 AN: 43456

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Benign	-0.24	T
BayesDel_noAF	Benign	-0.58
CADD	Benign	14
DANN	Benign	0.96
DEOGEN2	Benign	0.0016	T
Eigen	Benign	-0.87
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.082	N
LIST_S2	Benign	0.39	T
M_CAP	Pathogenic	0.31	D
MetaRNN	Benign	0.049	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.81	L
PhyloP100		0.0020
PrimateAI	Pathogenic	0.85	D
PROVEAN	Benign	0.040	N
REVEL	Benign	0.058
Sift	Benign	0.51	T
Sift4G	Benign	0.53	T
Polyphen		0.0040	B
Vest4		0.082
MutPred		0.097		Loss of helix (P = 0.028)
MVP		0.068
MPC		1.1
ClinPred		0.096	T
GERP RS		1.1
Varity_R		0.040
gMVP		0.17
Mutation Taster		=85/15	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: rs1316008005; hg19: chr1-26488480;