chr2-49455802-G-T

Variant names:

• chr2-49455802-G-T
• rs6726786
• ENST00000753905.1:n.242-942C>A

Variant summary

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

The ENST00000753905.1(ENSG00000282998):​n.242-942C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0698 in 151,848 control chromosomes in the GnomAD database, including 417 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 0.070 (417 hom., cov: 32)
• Consequence: ENSG00000282998 ENST00000753905.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 2 publications found

Genes affected

ENSG00000282998 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.0959 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753905.1. 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
	ENSG00000282998	ENST00000753905.1		n.242-942C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10596 AN: 151730 Hom.: 417 Cov.: 32

Gnomad AFR AF: 0.0398

Gnomad AMI AF: 0.0692

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0259

Gnomad FIN AF: 0.0818

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0979

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0698 AC: 10593 AN: 151848 Hom.: 417 Cov.: 32 AF XY: 0.0662 AC XY: 4916 AN XY: 74214

African (AFR) AF: 0.0398 AC: 1650 AN: 41476

American (AMR) AF: 0.0472 AC: 718 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 362 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0257 AC: 124 AN: 4820

European-Finnish (FIN) AF: 0.0818 AC: 864 AN: 10558

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0979 AC: 6637 AN: 67808

Other (OTH) AF: 0.0693 AC: 146 AN: 2108

Alfa AF: 0.0833 Hom.: 133

Bravo AF: 0.0644

Asia WGS AF: 0.0120 AC: 40 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.81
DANN	Benign	0.40
PhyloP100		-0.42

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: rs6726786;

hg19: chr2-49682940;