rs6743271

Positions:

• chr2-199796431-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FTCDNL1	NM_001350854.2	c.*20-35596C>T		intron_variant			NP_001337783.1
FTCDNL1	NM_001350855.2	c.212-35596C>T		intron_variant			NP_001337784.1
FTCDNL1	XM_024452852.2	c.397+23141C>T		intron_variant			XP_024308620.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FTCDNL1	ENST00000416668.5	c.212-35596C>T		intron_variant		1		ENSP00000454447
FTCDNL1	ENST00000420922.6	c.*20-35596C>T		intron_variant		5		ENSP00000456442	P1
FTCDNL1	ENST00000642693.1	n.406-10853C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.567

Gnomad4 OTH AF: 0.448

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.52

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

Publications

LitVar

Other links and lift over

dbSNP: rs6743271; hg19: chr2-200661154;