3-95687787-T-C

Variant names:

• chr3-95687787-T-C
• rs6806361
• ENST00000463799.2:n.85-3853A>G

Variant summary

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

The ENST00000463799.2(MTHFD2P1):​n.85-3853A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.329 in 152,086 control chromosomes in the GnomAD database, including 8,458 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 0.33 (8458 hom., cov: 32)
• Consequence: MTHFD2P1 ENST00000463799.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610
• Publications: 1 publications found

Genes affected

MTHFD2P1 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000463799.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTHFD2P1	ENST00000463799.2	TSL:3	n.85-3853A>G		intron	N/A
	MTHFD2P1	ENST00000785187.1		n.88-5043A>G		intron	N/A
	MTHFD2P1	ENST00000785188.1		n.64-3848A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50065 AN: 151968 Hom.: 8453 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.329 AC: 50092 AN: 152086 Hom.: 8458 Cov.: 32 AF XY: 0.330 AC XY: 24508 AN XY: 74352

African (AFR) AF: 0.348 AC: 14429 AN: 41476

American (AMR) AF: 0.230 AC: 3512 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3468

East Asian (EAS) AF: 0.416 AC: 2148 AN: 5164

South Asian (SAS) AF: 0.367 AC: 1767 AN: 4820

European-Finnish (FIN) AF: 0.381 AC: 4031 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.331 AC: 22494 AN: 67970

Other (OTH) AF: 0.299 AC: 631 AN: 2110

Alfa AF: 0.342 Hom.: 1176

Bravo AF: 0.316

Asia WGS AF: 0.430 AC: 1491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.52
PhyloP100		-0.061

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6806361; hg19: chr3-95406631;