rs10203122

Variant names:

• chr2-199831723-T-C
• rs10203122
• NM_001363886.2:c.212-11966A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001363886.2(FTCDNL1):​c.212-11966A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 151,982 control chromosomes in the GnomAD database, including 2,267 homozygotes. 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 0.16 (2267 hom., cov: 32)
• Consequence: FTCDNL1 NM_001363886.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 3 publications found

Genes affected

FTCDNL1 (HGNC:48661): (formiminotransferase cyclodeaminase N-terminal like) Predicted to enable folic acid binding activity and transferase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363886.2. 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
	FTCDNL1	NM_001363886.2	MANE Select	c.212-11966A>G		intron	N/A	NP_001350815.1	H3BUS8
	FTCDNL1	NM_001350853.2		c.212-11966A>G		intron	N/A	NP_001337782.1	E5RQL4
	FTCDNL1	NM_001350854.2		c.*19+12657A>G		intron	N/A	NP_001337783.1	H3BRX2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000420128.6	TSL:5 MANE Select	c.212-11966A>G		intron	N/A	ENSP00000457780.1	H3BUS8
	FTCDNL1	ENST00000622774.2	TSL:1	c.212-11966A>G		intron	N/A	ENSP00000482786.1	E5RQL4
	FTCDNL1	ENST00000416668.5	TSL:1	c.211+14352A>G		intron	N/A	ENSP00000454447.1	H3BMM2

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24490 AN: 151864 Hom.: 2266 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.185

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.161 AC: 24524 AN: 151982 Hom.: 2267 Cov.: 32 AF XY: 0.162 AC XY: 12069 AN XY: 74274

African (AFR) AF: 0.178 AC: 7364 AN: 41434

American (AMR) AF: 0.281 AC: 4291 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1531 AN: 5170

South Asian (SAS) AF: 0.120 AC: 578 AN: 4818

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10558

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8520 AN: 67960

Other (OTH) AF: 0.185 AC: 391 AN: 2108

Alfa AF: 0.140 Hom.: 1783

Bravo AF: 0.180

Asia WGS AF: 0.203 AC: 704 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.44
DANN	Benign	0.39
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

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: rs10203122; hg19: chr2-200696446;