rs6743271

Variant names:

• chr2-199796431-G-A
• rs6743271
• ENST00000416668.5:c.212-35596C>T

Variant summary

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

The ENST00000416668.5(FTCDNL1):​c.212-35596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,988 control chromosomes in the GnomAD database, including 18,092 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 0.46 (18092 hom., cov: 32)
• Consequence: FTCDNL1 ENST00000416668.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416668.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	NM_001350854.2		c.*20-35596C>T		intron	N/A	NP_001337783.1
	FTCDNL1	NM_001350855.2		c.212-35596C>T		intron	N/A	NP_001337784.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FTCDNL1	ENST00000416668.5	TSL:1	c.212-35596C>T		intron	N/A	ENSP00000454447.1
	FTCDNL1	ENST00000420922.6	TSL:5	c.*20-35596C>T		intron	N/A	ENSP00000456442.1
	FTCDNL1	ENST00000642693.1		n.406-10853C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69345 AN: 151870 Hom.: 18092 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.552

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.456 AC: 69357 AN: 151988 Hom.: 18092 Cov.: 32 AF XY: 0.464 AC XY: 34484 AN XY: 74282

African (AFR) AF: 0.196 AC: 8111 AN: 41448

American (AMR) AF: 0.451 AC: 6891 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.486 AC: 1684 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2998 AN: 5160

South Asian (SAS) AF: 0.552 AC: 2664 AN: 4824

European-Finnish (FIN) AF: 0.672 AC: 7095 AN: 10560

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38541 AN: 67944

Other (OTH) AF: 0.448 AC: 945 AN: 2110

Alfa AF: 0.512 Hom.: 3611

Bravo AF: 0.423

Asia WGS AF: 0.553 AC: 1921 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-0.45
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: rs6743271; hg19: chr2-200661154;