2-240639691-G-T

Variant names:

• chr2-240639691-G-T
• rs4676406
• ENST00000847200.1:n.215-3763C>A

Variant summary

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

The ENST00000847200.1(ENSG00000310104):​n.215-3763C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,012 control chromosomes in the GnomAD database, including 22,521 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 0.53 (22521 hom., cov: 33)
• Consequence: ENSG00000310104 ENST00000847200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 24 publications found

Genes affected

ENSG00000310104 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.93 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000847200.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310104	ENST00000847200.1		n.215-3763C>A		intron	N/A
	ENSG00000310104	ENST00000847201.1		n.215-3763C>A		intron	N/A
	ENSG00000310104	ENST00000847202.1		n.616-3763C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80836 AN: 151892 Hom.: 22485 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.335

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.532 AC: 80929 AN: 152012 Hom.: 22521 Cov.: 33 AF XY: 0.542 AC XY: 40296 AN XY: 74306

African (AFR) AF: 0.444 AC: 18417 AN: 41436

American (AMR) AF: 0.587 AC: 8977 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.335 AC: 1161 AN: 3470

East Asian (EAS) AF: 0.952 AC: 4925 AN: 5174

South Asian (SAS) AF: 0.689 AC: 3323 AN: 4822

European-Finnish (FIN) AF: 0.649 AC: 6864 AN: 10576

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35609 AN: 67932

Other (OTH) AF: 0.491 AC: 1038 AN: 2112

Alfa AF: 0.530 Hom.: 72314

Bravo AF: 0.522

Asia WGS AF: 0.791 AC: 2748 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	0.72
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4676406;

hg19: chr2-241579108;